🚧Guide Migration in Progress – Please be patient as I work to update and mirror my full collection of guides from Nexus Mods over to Modding.wiki. If a page is published and accessible, it is verified and ready for use. However, this notice will remain at the top of all pages until the entire migration is complete and all guides have been fully synchronized.
🏷️Guide version: 1.0.0 (📅02/25/2026)
🐉Skyrim versions: SSE 1.5.97 | SSE 1.6.x | VR
Full 🗒️changelog available at end of guide
Mod Manager Fundamentals (MO2)
An infernalryan Skyrim Modding Guide
¶ Overview
This guide provides an overview of mod managers and how they are used in Skyrim modding. It covers what a mod manager is, common modding terminology, and basic concepts and procedures used when managing mods. This is not a full tutorial, but should provide all context required to follow the steps and instructions used throughout my other guides. It is intended to serve as a reference rather than a complete walkthrough to read from start to finish. Feel free to skim the sections for anything new or useful, and 🔖Bookmark this page so you can quickly return later as needed.
This is the fundamentals guide for 🔷Mod Organizer 2. See below for other versions:
- For 🔶Vortex users, 🔗click here.
🎯Guide Contents:
- What a mod manager is, why it is recommended, and how it benefits a modded setup
- Modding terminology and how it is used in my guides
- How mods are loaded and the order different files are processed
- Mod manager usage covering the user interface, common tasks, conflict resolution, and plugin sorting options
- Additional notes and considerations for modding and mod manager behavior
- Changelog including full revision history of this document
Please consider 👍ENDORSING if you found this guide helpful!
🧠IMPORTANT NOTE – In this guide, there are references to your 📁[🐉Skyrim] folder as well as your Skyrim 📁[🐉Data] folder. These are special folders (denoted by brackets and a dragon icon) that refer to your specific root Skyrim game folder and its 📁Data folder inside. For example, if you install Skyrim into 🖥️C:\Games\Steam, 📁[🐉Skyrim] would refer to 🖥️C:\Games\Steam\steamapps\common\Skyrim Special Edition, and 📁[🐉Data] would refer to 🖥️C:\Games\Steam\steamapps\common\Skyrim Special Edition\Data. Paths will vary for GOG and VR users.
¶ 1. What is a mod manager?
A mod manager is a tool that installs, organizes, and controls mods for a game without permanently mixing them into the game's files. Instead of copying files directly into your game directory, it acts as a middle layer between the game and your mods and manages how they are added and the order in which they are applied. Each mod manager handles this differently, but the underlying function is largely the same—Mods are stored in a staging folder outside of the game directory, and then deployed to the game based on user defined conflict rules and priorities. In addition, mod managers also support profiles for switching between different setups or testing changes without affecting your main game.
The primary purpose of a mod manager is to manage plugin load order and file conflicts, showing which mods override others and giving you control over the final result. Understanding file and plugin interactions and conflict resolution is a normal and expected part of modding. Without a mod manager, your mod list can become difficult to maintain, especially as your mod list grows. While all mod managers provide this core functionality, their other features and how they are implemented are what give each its own distinct feel or flavor (it's why some users prefer one over the other).
While it is possible to perform modding without a mod manager, manually installing mods hides conflicts, makes changes difficult to undo, and makes it much harder to troubleshoot when something breaks. A mod manager keeps your base game folders clean, makes conflicts visible, and allows you to safely experiment without permanently committing changes. For anything beyond the simplest setups, a mod manager becomes a necessity.
¶ 2. Modding terminology
Modding uses a number of common terms, and some of them are used a little differently depending on the mod manager or context. For consistency, this section clarifies how they are used throughout my guides. The entries are short and formatted to be easy to skim, so feel free to ⏩️Skip to section 3 if you're already familiar with them.
¶ 2.1. Basic terms
These are the most common terms used when modding Skyrim.
- Mod – A package that changes or adds content to the game. A mod can include files, plugins, or both.
- Plugin / game plugin – A file that contains data records loaded by the game and used to change gameplay, quests, items, NPCs, or other game data. Plugins have .esm, .esp, or .esl file extensions. The term plugin is sometimes used interchangeably with mod, but more specifically refers to this type of game file. Below are the plugin types used by Skyrim:
- ESM (Elder Scrolls Master) – A plugin file type intended to load early in the load order. While ESM files are typically used as masters for the purpose of dependencies, being an ESM does not inherently require other plugins to depend on it.
- ESP (Elder Scrolls Plugin) – The standard plugin file type used to make changes to the game.
- ESL (Elder Scrolls Light) – A lightweight plugin file type designed to reduce load order usage. These plugins do not count toward the traditional plugin limit, but they are limited in how many records they can contain, which is what makes them light.
- ESPFE (ESL-flagged ESP) – An ESP file that has been flagged as ESL, allowing it to behave like a light plugin while still using the ESP file format.
- SKSE plugin – A special type of plugin designed to work with the Skyrim Script Extender (SKSE) that expands the game's functionality beyond what is possible with standard plugins. SKSE plugins are .dll files. Despite the name, these are different from typical game plugins and do not appear in the plugin list.
- Assets – Other (non-plugin) game files that control how things look and behave in-game. This can include meshes (.nif—which are 3D models), textures (.dds), scripts (.pex), sounds (.wav, .xwm), interface files (.swf), and configuration files (.ini), to name a few.
- Archive / BSA – This is a .bsa archive file (similar to .zip) that packages game assets.
- Master – Masters are game plugins that another plugin depends on, and they must be loaded before that plugin in order for it to function correctly.
- Mod list – A general term used to refer to a collection of installed mods. This also refers to the literal list of mods in your chosen mod manager.
- Plugin list – A term used to describe the list of game plugins loaded by the game.
- Executable / tool – These are external programs launched by the mod manager, such as SKSE, xEdit, or DynDOLOD. Though these terms can be used interchangeably, officially, these are known as executables in Mod Organizer 2, and tools in Vortex.
¶ 2.2. Load order terms
The term load order can be ambiguous as it is commonly used to describe multiple things. It may refer to the order in which plugins are loaded, to mod priority for Mod Organizer 2 users, or more generally to a mod setup as a whole (for example, "My load order has over 1,000 mods"). To avoid confusion, when this term is used in my guides, additional context will be provided where needed to make the meaning clear, or one of the more specific terms below may be used instead.
- Plugin load order / plugin order – Refers specifically to the order in which .esm, .esp, and .esl plugin files are loaded.
- Priority (MO2 only) – In Mod Organizer 2, priority refers to the numeric value that determines load order, from lowest to highest. In the mod list, priority controls loose file conflict resolution. In the plugin list, priority reflects plugin load order. In my guides, this term may also be used in conjunction with the list it refers to, such as mod list priority or plugin list priority, to provide clarification when needed.
¶ 2.3. Conflict resolution terms
A conflict occurs when two or more mods attempt to modify the same files or plugin records. Since the game can only use a single version, one must take precedence over the others. Which version wins depends on the type of conflict. Loose file conflicts are resolved by the mod manager's priority or rule system, while plugin records and BSA-based conflicts are determined by plugin load order. Throughout my guides, instructions are provided to resolve conflicts that arise when adding mods or files to your mod list, and the terms below are used in those steps.
- Overwrites – This is the most direct term used to describe one mod replacing another mod's files or records and winning the conflict (e.g., Mod A overwrites Mod B).
- Before / after – Indicates the relative order in which mods or plugins are applied. Something that loads after another entry takes precedence and wins the conflict, while something that loads before another entry loses the conflict and has its data overwritten. These terms are applicable to both files and plugins, and are used directly in Vortex's conflict resolution dialog.
- Lower / higher priority (MO2 only) – Refers to the priority value in Mod Organizer 2. Something with a higher priority loads after another entry, takes precedence, and wins the conflict, while something with a lower priority loads before another entry and loses the conflict. These terms are applicable to both file conflicts and plugin load order in MO2.
- Positional language – Positional terms such as top, bottom, higher, or lower can be ambiguous on their own, as their meaning depends on how plugin or mod lists are sorted. If one of these terms is used in my guides, it will always be accompanied by additional context (such as explicit sorting assumptions) to ensure the intended meaning is clear. These terms are NOT the same as lower / higher priority (above).
¶ 3. How mods are loaded
Mod managers control which files the game sees and in what order, but different types of files are handled differently by the game engine itself. See below.
- Plugin files (.esm, .esp, .esl) – The mod manager updates the 📄plugins.txt file to reflect your configured load order of these plugins. This order is used to resolve record conflicts as well as BSA-level file conflicts. When multiple plugins modify the same record, the plugin that loads last takes precedence.
- Archive files (.bsa) – These files (e.g., 📄PluginName.bsa) are loaded alongside their associated plugin (e.g., 📄PluginName.esp) and follow that plugin's position in the load order. This means that file conflicts between mods contained within these archives are resolved based on plugin load order, NOT by mod list priority or loose file conflict rules. In fact, Vortex doesn't even have a way to display BSA-level conflicts. If you need the contents of one BSA file to overwrite another, its plugin must load after the other plugin, or you can use loose files to override them instead.
- Loose files – These are handled separately and always take precedence over files inside BSA archives, regardless of plugin load order. Loose file conflicts are resolved entirely within the mod manager itself, using mod list priority in MO2 or conflict rules in Vortex, rather than plugin order.
- INI files (.ini) – The base configuration files 📄Skyrim.ini and 📄SkyrimPrefs.ini are loaded when the game starts, followed by 📄SkyrimCustom.ini if it exists, which also loads at startup and allows you to override any values from the other two without permanently modifying them. Skyrim also supports plugin specific INI setting overrides, where a plugin such as 📄PluginName.esp will automatically load a matching 📄PluginName.ini if one exists and apply its values when loaded. These INI files follow the same rules as record conflicts, so a value from the last loaded file wins when the same setting is defined in multiple files. This is important to know because if a change to your base configuration files or 📄SkyrimCustom.ini does work as intended, another mod may be overriding that value with its own INI file.
¶ 4. Mod manager usage
This section covers common tasks when using 🔷Mod Organizer 2, along with an overview of the interface, handling Nexus downloads, adding external tools, profile management, and other helpful information.
¶ 4.1. Main interface overview
⏩️Skip to section 4.2 if you are already familiar with the Mod Organizer 2 interface, otherwise, proceed below (↕️Expand the 📖Continue reading block). This section provides a (very) brief, high-level overview of some key interface elements for definition and orientation-purposes only. Not all areas are covered here, as some elements are simply shortcuts or menus, or are otherwise not used in my guides, while others are explained in more detail later when referenced. This list is not intended to be exhaustive.
📖Continue Reading: (↕️Expand for details)
- Menu bar – This is the horizontal strip at the top of the main application window containing dropdown menus (File, Edit, etc.).
- Main toolbar – This is the icon bar at the top of the screen which contains shortcuts to some commonly accessed menus, panels, or actions, such as settings, plugins, and executables.
- Key elements include:
- Notifications icon – The warning icon on the right displays important warnings or errors related to your load order when a numbered badge is present. This is covered in more detail later.
- Left icons – These are shortcuts to some commonly accessed menus, panels, or actions, such as settings, MO2 plugins, and executables.
- INI Editor – This tool allows you to easily modify the game INI files for the currently active profile. It can be accessed from the puzzle icon in the main toolbar by selecting INI Editor from the list.
- This is also accessible via the Tools > Tool Plugins menu in the main menu bar.
- Left pane – This is the left side of the main application window.
- Key elements include:
- Mod list – This is the main list of managed and installed mods.
- Profile list – This is the dropdown above the mod list used for profile management.
Wrench button – Icon to the right of the profile list. This is a shortcut menu for actions performed for all mods in the mod list.
Folder button – Icon to the right of the Wrench button. This is a shortcut menu for important folders. Of note, from here you can quickly open the following:- Game folder – This is your 📁[🐉Skyrim] folder.
- MyGames folder – Your Skyrim folder in 📁Documents.
- Mod folder – This is the staging folder where your mods are installed and managed.
- INI folder – This always opens the folder where your 📄Skyrim.ini, 📄SkyrimPrefs.ini, and 📄SkyrimCustom.ini files reside in for the current profile.
Backup / 
Restore buttons – The icons to the right of the Folder button. These allow you to create and restore backups of your current mod list, preserving mod priority order and enabled or disabled status. These buttons function similarly in the Plugins tab.- Active mod count – Shows the total number of active mods in your mod list.
- Filter text box – Apply a custom text filter to the mod list.
- Right pane – This is the right side of the main application window.
- Key elements include:
- Executables list – This is the large dropdown box at the top of the pane used for managing your list of executables.
- Run button – 🚀Launch the currently selected executable.
- Plugins tab – This is the list of installed game plugins. Additionally, you can 🗃️Sort mods with LOOT, and create and restore backups from this tab.
- Archives tab – Shows a list of BSA archives and their associated plugin. Right-clicking a BSA file allows you to 📦Extract the files from it.
- Data tab – Displays what the final virtual 📁[🐉Data] folder created by MO2 will contain with the current selection of mods and file overrides. You can filter this list to show or hide BSA archives or hidden files, display only conflicts, or apply a custom text filter. Many common actions can be performed from this list.
- Files with conflicts are displayed in red.
- Saves tab – Shows a list of save games associated with the current profile.
- Downloads tab – Shows a list of files downloaded from Nexus or added manually to MO2, along with their current status and other details. Many common actions can be performed from this list.
- Mod information dialog – Provides additional information about the mod being viewed. Opens when you double-click an entry in the mod list or plugin list, or when selecting Information… or Open Origin Info… from the respective right-click context menu.
- Key elements include:
- Text Files / INI Files tabs – Allows you to view and edit files included in the mod directly within the tab.
- Conflicts tab – Allows you to view and manage loose file conflicts for the current mod within the tab. This is covered in greater detail later in this guide.
- Notes tab – This allows you to create custom notes for the given mod. These notes appear in the mod list if their respective columns are shown.
- Filetree tab – Displays a list of all files and folders included with the mod. Many common actions can be performed from this list.
¶ 4.2. Handle download links on Nexus
⏩️Skip to section 4.3 if you are already familiar with this process, otherwise, proceed. The steps below ensure the option to download directly to your mod manager are enabled. When you open MO2, if nxm:// links are not associated with the program, it will ask if you would like to (re-)associate them. Clicking Yes is typically all you need to do, but there may be times where you may have to perform the steps below manually.
- From the Tools menu, click Settings….
- Within the Nexus tab of the settings dialog that appears, verify that MO2 is connected to your Nexus account. This should be done automatically during installation, but if the Nexus Account box does not contain your User ID and Name, click the Connect to Nexus button and follow the directions to authenticate your account (this will open a web browser).
- Logging in is required for mod manager downloads to work.
- After verifying login, click the Associate with "Download with manager" links button.
- If you had to (re-)connect your Nexus account, MO2 will prompt you to restart the program. Do this now.
- ✔️You are done!
¶ 4.3. Adding new executables to MO2
⏩️Skip to section 4.4 if you already have an understanding of how to add executables to MO2, otherwise, proceed. This process is required for any application that needs to interact with your mod list.
💡Additional information: (↕️Expand for details)
Mod Organizer 2 uses a Virtual File System (VFS), which is why executables must be added and launched in this way. Launching the game or tools outside of MO2 means they will not see any of the files MO2 is managing and will not function correctly. For a more detailed explanation of how the VFS works and why this is necessary, see ⬇️section 5 (Additional notes).
- Within MO2, click the executables dropdown (next to the Run button), and select <Edit...> (default executables for SSE are shown, yours may differ).
- Alternatively, you can click the gear icon in the main toolbar
- In the Modify Executables dialog that opens, click the plus (➕) icon on the left and select Add from file....
- Fill in all necessary fields and click the OK button to save.
- NOTE – When adding executables in my other guides, all necessary fields or exceptions will be included in each respective step's instructions.
- As an additional tip, clicking the Shortcut button (below Run) and selecting Toolbar and Menu will add a shortcut to the currently selected executable to both the main toolbar and menu bar. You can also add shortcuts to the other locations listed.
- The toolbar shortcuts appear on the top right of the main toolbar, to the left of the separator, and look like this (your shortcuts may vary):
- The menu bar shortcuts are added to the Run menu and look like this (your shortcuts may vary):
- ✔️You are done!
¶ 4.4. Launching Skyrim
⏩️Skip to section 4.5 if you already know how to launch Skyrim from MO2, otherwise, proceed. Note that when using mod managers, you MUST launch the game via its respective SKSE loader location. This is how you will launch the game each and every time you wish to play (with mods).
- Ensure you have Skyrim Script Extender (SKSE) installed and added as an executable in MO2.
- Review and address any active warnings on the notification icon in the main toolbar.
- Do NOT start the game if missing masters are indicated. These are likely to cause a crash during gameplay.
- Select the SKSE executable you set up in previous steps (or that came with your 🧀Wabbajack installation) from the executables dropdown list. For example:
- Click the Run button.
- ✔️You are done!
¶ 4.5. Mod list
The mod list is where mods are installed, managed, and configured, and loose file conflicts are handled. The steps below explain how mods are managed in the mod list, with references to other panels and dialogs as needed.
¶ 4.5.1. Basic operations
⏩️Skip to section 4.5.2 if you already familiar with how to 🛠️Install, 💣Uninstall, ✅Enable, and ⛔Disable mods, and 🗑️Delete archive files in MO2, otherwise, proceed.
- When you download a mod using the Mod manager download button on the Nexus mod page when MO2 is open, the mod will appear in the Downloads tab on the right side of the main MO2 window.
- To manually add a mod to the list for installation, 👆Drag a file into this tab. This must be an archive file (.zip, .7z, .rar, etc.).
- NOTE – This process of adding files manually to MO2 is required in several steps throughout my guides, as well as anytime you need to add your own custom mods or manually downloaded files, or modify an existing mod (to remove files, for example). Alternative methods for non-archives may be covered in my guides where appropriate, but these aren't typically required for most setups and are used only when more efficient.
- To 🛠️Install a mod, double-click the entry in the Downloads list.
- Alternatively, you can right-click the entry and choose Install from the menu.
- Some mods include an FOMOD installer that allows you to select specific options or patches. Follow the on-screen prompts to choose your preferences and click the Install (or similar) button on the final screen to complete the process.
- Installing a mod with one of the above methods will add the mod to your mod list and assign it the highest priority.
- If you want more granular control when installing, you can 👆Drag a file from the Downloads tab into the mod list to install it at a specific position in the priority order.
- To ✅Enable or ⛔Disable mods, toggle the checkbox next to the entry in the mod list.
- These actions can be performed for all mods in the list from the All Mods > option in the right-click context menu of any mod.
- To 💣Uninstall a mod, right-click the entry in the mod list and select Remove Mod… from the menu.
- NOTE – This does not remove the downloaded archive file.
- To 🗑️Delete an archive file (the .zip or .7z file downloaded from Nexus), right-click a mod in the Downloads tab and select Delete.
- Alternatively, to remove multiple files at once, right-click and select Reveal in Explorer, and manage the files from there.
- You can 👆Drag mods directly to a new position in the mod list to change its priority.
- If dragging a mod into a separator, it will be given the highest priority of all mods also inside that separator.
- As an alternative to dragging, you can right-click the entry and select Send to… for the following options:
- Lowest Priority – The plugin is given the lowest priority in the mod list, allowing all other mods to overwrite its loose files when conflicts occur. With default sorting enabled, this places the mod at the top of the list.
- Highest Priority – The plugin is given the highest priority in the mod list, allowing it to overwrite loose files of all other mods when conflicts occur. With default sorting enabled, this places the mod at the bottom of the list.
- Priority – This applies an explicit priority to the mod, moving it to this position in the mod list.
- Separator – This moves the plugin to the highest priority inside of the selected separator.
- Multiple entries can be selected using the Shift and Ctrl keys, allowing you to select ranges of entries with Shift or individual entries with Ctrl.
- If a mod contains a plugin file, selecting its entry in the mod list will highlight the plugin's position in the plugin list (including the scrollbar). This makes it easy to locate.
- To create a new empty mod (folder), click the wrench icon at the top right of the mod list and select Create empty mod.
- In the dialog that comes up, enter a name and click the OK button. This new empty mod will be created with the highest priority.
- Alternatively, you can also perform the above by right-clicking a mod in the mod list, and selecting All mods > Create empty mod above. This creates an empty mod at the selected mod's priority, shifting the priorities of all mods that load after it accordingly.
- Empty mods create a blank mod folder that you can use to manually add and manage files. They are useful for testing new files or small changes without packaging them into a .zip and installing them through the Downloads tab. They're also especially helpful for organizing and managing files from the Overwrite folder.
- To quickly open a mod in Windows Explorer, hold down the ctrl key and double-click the entry in the mod list.
- This makes it easy to add files to an existing or empty mod.
- If files are added or removed from Windows Explorer, you must either click the Refresh icon in the main toolbar or press the F5 key in MO2 to refresh its view of the files being managed.
- To toggle which columns are visible in the mod list, right click any column header and select or deselect your desired options.
- To create a backup of a mod in the list, right-click the entry in the mod list and select Create Backup. This is useful if you plan on modifying files in a mod and want a way to revert those changes, as well as other use cases.
- This creates a snapshot of the mod in its current state as a separate entry in the mod list called ModName_backup.
- Though it appears in the list, this mod is not loaded into the game.
- Right-clicking the entry will allow you to restore or remove the backup. Restoring will replace the original mod with the backed up version.
- Additional Tips:
- If you need to change your original FOMOD selections for a mod you've installed—such as after adding a new mod which that FOMOD also has a patch for—perform a 🛠️Reinstall. This can be done by repeating the standard installation steps or by right-clicking the mod in your mod list and selecting Reinstall mod.
- It is recommended to 🗑️Delete downloaded archives for mods that do not use a FOMOD installer to save disk space. Since these mods lack installation options, the archive is no longer necessary once the mod is installed and enabled.
- Remember that uninstalling a mod and deleting its download archive are separate from one another. All archives remain in the download folder until they are manually removed.
¶ 4.5.2. Separators
⏩️Skip to section 4.5.3 if you are already familiar with the process of creating and using separators in MO2, otherwise, proceed. Separators are collapsible sections that help organize mods, keeping them grouped together and logically distinct from others.
- To create a new separator, click the wrench icon at the top right of the mod list and select Create separator.
- In the dialog that comes up, enter a name and click the OK button. This new separator will be created with the highest priority.
- Alternatively, you can also perform the above by right-clicking a mod in the mod list, and selecting All mods > Create separator above. This creates a separator at the selected mod's priority, shifting the priorities of all mods that load after it accordingly.
- You can 👆Drag mods directly into this separator or right-click an entry and select Send to… > Separator… to move them.
- The separator color can be changed by right-clicking the entry in the mod list and selecting Select Color… from the context menu. This can help with quickly identifying a separator at a glance.
- These colors also appear in the right scrollbar in the mod list.
- To reset the separator color, select Reset Color from the right-click context menu.
¶ 4.5.3. The Overwrite folder
⏩️Skip to section 4.5.4 if you are already familiar with managing the Overwrite folder in MO2, otherwise, proceed. The Overwrite folder contains files generated at runtime or created by tools if they are not explicitly assigned to a mod. This commonly includes logs, configuration files, and tool output. Below are instructions and tips on how to manage this folder.
💡Additional information: (↕️Expand for details)
As a practical example, some mods do not create their base configuration files until the game is launched for the first time. In these cases, the file does not exist in the mod's installed files and is instead generated at runtime. Because the file did not previously exist and is not associated with any specific mod, Mod Organizer 2 places it in the Overwrite folder. This behavior is expected and simply indicates that the file was created during gameplay rather than installation. The typical approach to resolve this is to 👉Move the file into a new or existing mod so it becomes part of the managed mod list rather than remaining in Overwrite.
- The Overwrite folder is located at the very bottom of the MO2 mod list. Double-clicking the entry will open the folder.
- If files exist in this folder, a numbered badge will be displayed on the notifications icon in the top right of the main toolbar. Open the notifications by clicking the icon to confirm that the entry specifically references the Overwrite directory, as shown below.
- To properly manage this folder, 👉Move each file in the Overwrite directory into another mod in the mod list, when applicable. Doing so assigns the file to a specific mod and prevents it from continuing to appear in Overwrite. Files can be placed into one of the following:
- An existing mod – For example, a configuration file generated by the Floating Subtitles mod can be moved directly into the Floating Subtitles entry in the mod list to keep it included with the main mod.
- A new empty mod – For example, you can create a new empty mod, such as Floating Subtitles - Configuration Files, and place the configuration file there to keep it separate from the main mod entry.
- The easiest way to 👉Move files properly is to open the Overwrite folder and 👆Drag the desired file directly from Overwrite into the mod you want to contain it in the mod list.
- This method preserves the file's full directory path from Overwrite, so you do not need to recreate the required folder structure manually.
- The Sync to Mods… option in the right-click context menu of the Overwrite entry is not recommended as it can be inconsistent and does not reliably detect all file types or structures that should be moved out of the Overwrite folder.
- Sometimes identifying which file(s) belong to which mods is not intuitive. For these, you may need to perform a web search to help.
- It is recommended to update the following options under Settings > Plugins, and then selecting the Basic diagnosis plugin plugin:
- ow_ignore_empty – When set to true, this option will ignore empty folders when determining if there are files in Overwrite.
- ow_ignore_log – When set to true, this option will ignore log files when determining if there are files in Overwrite.
- Do not worry if you cannot keep the Overwrite folder completely clean. The main goal is to keep known files assigned to mods, rather than leaving them in Overwrite. Using the above options should help with this.
¶ 4.5.4. Resolving file conflicts
⏩️Skip to section 4.6 if you are already familiar with how to resolve loose file conflicts in MO2 (including individual file exceptions!), otherwise, proceed. File conflicts in Mod Organizer 2 are resolved based on a mod's priority in the mod list. When two or more mods contain the same loose file(s), the mod with the higher priority always wins. Additionally, you can further refine this behavior by creating overrides for individual files when necessary. Many users find this approach more straightforward and intuitive than manually creating rules for each mod, as is required with Vortex.
📣NOTICE – By default, Mod Organizer 2 sorts the mod list by ascending priority (lowest to highest), indicated by a ^ symbol in the Priority column header. This is always the recommended way to sort mods, as it mirrors the familiar top-down behavior of plugin load order. With this sorting method, higher-priority mods appear lower in the list and win file conflicts, in the same way that later-loading plugins win conflicts between plugin records and BSA-based conflicts.
¶ 4.5.4.1. Conflicts overview
This section explains how to identify conflicts and manage them directly from the mod list. MO2 uses several visual indicators to help you quickly identify when mods conflict with one another, including icons and row highlighting. Depending on your settings, BSA archive-related conflicts may also appear here alongside loose file conflicts, though their resolution is handled in the plugin list, not the mod list (see ⬇️section 4.6.3 (BSA-level conflicts)). It also covers how to open the conflicts dialog, where all file conflicts for the selected mod can be viewed.
- If a conflict exists for a mod, the Conflicts column will display one or more of the following icons. Separators will also show these icons when collapsed if the mods they contain have conflicts.
Overwrites loose files (yellow lightning bolt with a green plus sign)- This mod's loose files overwrite conflicting loose files from other mods.
Overwritten loose files (yellow lightning bolt with a red minus sign)- This mod's loose files are overwritten by conflicting loose files from other mods.
Loose files overwrites and overwritten (yellow lightning bolt with both a green plus sign and a red minus sign)- This mod's loose files overwrite some conflicting files and are overwritten by others.
Redundant (gray lightning bolt)- Every single file in this mod is being overwritten by other mods. This means it is not doing anything in your mod list.
Overwrites another archive file (yellow chest with a green plus sign)- Files in this mod's archive overwrite conflicting files in other archives.
Overwritten by another archive file (yellow chest with a red minus sign)- Files in this mod's archive are overwritten by conflicting files in another archive.
Archive file overwrites and overwritten (yellow chest with both a green plus sign and a red minus sign)- Files in this mod's archive overwrite some conflicting archive files and are overwritten by others.
Overwrites an archive with loose files (blue lightning bolt with a green plus sign)- This mod's loose files overwrite conflicting files in other archives.
Archive is overwritten by loose files (red chest with a red minus sign)- Files in this mod's archive are overwritten by loose files from another mod.
- To enable display of conflict icons pertaining to BSA archive files, go to Settings > Workarounds and select the ☑️ Enable archives parsing (experimental) option. This setting is recommended as it provides conflict information normally hidden in the MO2 interface. Although labeled experimental and noted to have negative effects on performance and known incorrectness in the tooltip, it is generally safe to use and provides additional valuable information.
- In addition to the icons shown for mods with file conflicts, selecting a mod entry in the mod list will highlight all other mods with files it overwrites or is overwritten by. This is especially useful for identifying them. Additionally, these mods will have their positions marked in the scrollbar on the right side of the mod list as well, making them easier to locate. The highlight colors are configurable under the Settings > Theme tab.
- The most direct way to change which mod wins a file conflict is to 👆Drag a mod to a new position in the list or adjust its priority using the right-click Send to… context menu. The mod with the higher priority value will win.
- To view specific file conflicts, double-click a mod in the list that displays one of the above conflict icons to open the mod information dialog.
- Alternatively, you can right-click the mod entry and select Information….
- Conflicts are shown by clicking the Conflicts tab.
¶ 4.5.4.2. Detailed conflict information
While file conflicts themselves are managed based on a mod's priority in the mod list, you may want to view these conflicting items to see if any file-specific exceptions are necessary. This can be done in the Conflicts tab of the mod information dialog. Below are some details on the information available in this window.
- The below is an example of what the Conflicts tab of the mod information dialog looks like (your list will differ depending on the conflicts you have in your specific load order).
- On this screen, you'll find the following information and options of importance for managing conflicts.
- Winning file conflicts – All files this mod is overwriting and winning the conflict for are shown in this list, along with all other mods containing each file.
- Losing file conflicts – All files being overwritten by other mods are shown in this list, along with the Providing Mod, which is the single winning mod for this conflict (more on this under the Advanced tab entry).
- Filter – The lists of files can be filtered to display only matching results. This can be helpful if there are a lot of conflicts and you do not want to scroll through every entry in the list.
- Expand and Collapse icons – These icons next to the winning/losing/no conflicts headers, or their associated text can be clicked to collapse or expand their sections. This helps increase the viewable space for the list you are working with.
- The General tab only shows the single winning mod for each file conflict in the Losing file conflicts list (referred to as the Providing Mod). If your selected mod also overwrites a file but ultimately loses, or if it loses to multiple mods, this information won't be shown here. For a more detailed breakdown of file conflicts, use the Advanced tab.
- The highlighted information in the image above shows the mods being overwritten for a file conflict this mod is ultimately losing, which is not visible at all under the General tab. Similarly, if this file were being overwritten by more than just one mod, those mods would also be shown in the Overwritten By column.
¶ 4.5.4.3. Creating file-specific exceptions
While the priority order of your mods should accurately handle most file conflicts automatically, there may be cases where individual file exceptions are needed. For example, if one mod should overwrite another, but a single file from the overwritten mod must take precedence, you'll need to create an exception. Similarly, if adjusting a mod's position in the list isn't an option because it would disrupt other file conflicts, an exception may be necessary as well. See below for information on how MO2 performs this.
- File exceptions in MO2 are managed by hiding files. Simply put, if you want a lower-priority mod to win a file conflict, you can use MO2 to 🙈Hide the conflicting file in the higher-priority mod(s) that would otherwise overwrite it so that the lower-priority mod wins.
- When you 🙈Hide a file it, MO2 simply renames it (it doesn't actually disappear), eliminating the conflict since the filenames no longer match. This allows the valid file in the next-highest priority mod to take precedence (if one still exists). This process can be repeated as many times as needed until the file from the mod you want is the winner.
- Hiding files can be performed from most file list views in MO2, primarily, the Conflicts and Filetree tabs of the mod information dialog, as well as the Data tab on the right pane of the main MO2 window. Just right-click a file in one of these lists and select Hide. You can 👁️Unhide hidden files to remove the exception at a later time by selecting Unhide (or Un-Hide, depending on the list)from the right-click menu.
- Below is an example of the right-click context menu in the Conflict tab:
- Other notes:
- Hidden files are not visible in the Conflicts tab view so you cannot 👁️Unhide files there. You will have to use one of the other views instead.
- The ☑️ Hidden Files option must be selected below the Data tab to show hidden files from that view.
- Hidden files will be given the extension .mohidden.
- For example, if you hide 📄texture.dds, the filename will become 📄texture.dds.mohidden.
- If a mod in your mod list has file(s) hidden, you will see the following icon under the Flags column:
Contains hidden files (piece of paper)- A useful tip is that while in the Conflicts tab of the mod information dialog, you can right-click a file in the list, select Go to…, and choose a mod that is overwriting the file to be taken directly to that mod. From there, you can 🙈Hide files as needed to create an exception.
- If it is a mod with a lot of files, you may want to remember part of the filename to put into the filter box.
- The main drawback of hiding files is that a higher-priority mod installed later may overwrite the same files, requiring you to hide them again. For this reason, increasing the priority of the mod you want to win the conflict is usually the better solution when possible.
- One effective alternative to hiding files for handling file-specific exceptions is to create an empty mod and copy all applicable files to that mod instead. This treats the files as their own mod, which can be positioned more permanently in the mod list to overwrite any conflicts from future mods as well.
¶ 4.6. Plugin list
The plugin list contains a list of your plugins along with the order in which they load. Plugin load order is used specifically for record conflicts, as well as BSA-level file conflicts (loose file conflicts are handled in the mod list, not the plugin list). See below for more information.
📣NOTICE – In normal use, this view is mainly used for 🗃️Sorting plugins and other LOOT-related actions. In most cases, you should not need to enable or disable plugins independently of the mod that provides them. Plugin-level toggling is primarily intended for optional plugins, patches, or troubleshooting, and is rarely something you'll need to do regularly.
¶ 4.6.1. Basic operations
⏩️Skip to section 4.6.2 if you are already familiar with how to ✅Enable, ⛔Disable and perform other common tasks for mods in the plugin list, otherwise, proceed.
- To ✅Enable or ⛔Disable a mod, toggle the checkbox next to the entry in the plugin list.
- Alternatively, you can right-click one or more selected entries, and select Enable selected or Disable selected from the context menu.
- All plugins can be enabled or disabled at once as well from this same menu.
- Enabling or disabling a plugin does NOT forget its position in the plugin list, however, if the mod itself is disabled in the mod list, this position will be lost.
- Multiple entries can be selected using the Shift and Ctrl keys, allowing you to select ranges of entries with Shift or individual entries with Ctrl.
- Selecting an entry in the plugin list will highlight its position in the mod list (including the scrollbar). This makes it easy to find the mod that is supplying the plugin file.
- Hovering over an entry will display a tooltip which provides helpful information about the plugin. This includes details such as its enabled masters and if a BSA archive is loaded, when applicable. The tooltip may also include additional notes from the plugin’s applied Flags, such as if the ESP file is flagged as an ESL, if the plugin is a dummy file used only to load a BSA archive, and LOOT-related messages, among others.
- Double-clicking an entry in this list will bring up the mod information dialog.
- Alternatively, you can right-click an entry and select Open Origin Info… from the context menu.
- To toggle which columns are visible in the plugin list, right click any column header and select or deselect your desired options.
¶ 4.6.2. Adjusting plugin load order
⏩️Skip to section 4.6.3 if you are already familiar with how to 🗃️Sort plugins in Mod Organizer 2 to adjust load order, otherwise, proceed. MO2 comes pre-installed with 🔗LOOT, which allows plugin sorting using required masters and established load order rules maintained by the LOOT team and the wider modding community. This is usually sufficient for smaller mod lists, but larger or more complex setups may require some manual sorting to handle record conflicts correctly.
📣NOTICE – Before adjusting plugin order manually, the plugin list should always be sorted by ascending priority (lowest to highest), indicated by a ^ symbol in the Priority column header. This is the default MO2 sorting method. This order reflects the actual plugin load order from top to bottom, ensuring that the visual position of plugins in the list directly corresponds to when they load, with lower entries loading later and taking precedence for record and BSA-level file conflicts.
- The Sort button at the top left of the plugin list will automatically sort the plugins in the list using LOOT.
- This process is automatic once you confirm with the Yes button. There is no way to preview these results, so you may wish to backup your existing plugin load order using the Backup button at the top right of the list first in the event you need to restore it.
- If you want greater control over sorting, including the ability to create manual rules and preview changes before applying them, it is recommended to 🛠️Install and ⚙️Configure LOOT as an executable. While any rules created in the standalone LOOT application will be respected by MO2's built-in sorting, once installed, it is generally best to use the standalone application directly so this added functionality is always available. Adding a toolbar or menu shortcut also makes it more accessible than the built-in sort button (since it is persistent across tabs).
- You can 👆Drag plugins to directly move them to a new position in the plugin list.
- As an alternative to dragging, you can right-click the entry and select Send to… for the following options:
- Top – The plugin is moved as high as possible in the plugin list (with default sorting), applying the lowest valid priority allowed.
- Bottom – The plugin is moved to the bottom of the plugin list (with default sorting), applying the highest priority and loading after all other plugins.
- Priority – This applies an explicit priority to the plugin, attempting to move the plugin to that position in the plugin list.
- MO2 does not allow a plugin to load before any of its assigned masters. When using the manual sorting techniques above, if a plugin does not appear where you expect it to, or cannot be moved to that position, it may be due to this behavior. This is intentional, as loading a plugin before one of its configured masters is considered invalid.
- To lock a plugin's existing position in the plugin load order, right-click the entry and select Lock load order from the menu. This prevents any mods from loading before it, and it also prevents any existing mods that load before it from being moved as well, as this would change the locked mod's priority.
- Locked plugins must be unlocked before attempting to manually change their position or reorder plugins around them.
- When you ✅Enable or ⛔Disable mods in the mod list, this can cause a locked plugin to change priority when required by load order rules, such as when a newly enabled ESM plugin must load earlier, or when a plugin above a locked entry is removed and the list is compacted.
- This feature is best used sparingly, as locking multiple plugins can make manual sorting more difficult.
¶ 4.6.3. BSA-level conflicts
⏩️Skip to section 4.7 f you are already familiar with how to resolve BSA-level file conflicts in MO2, otherwise, proceed. BSA files load alongside their associated plugin files, so plugin load order determines conflict resolution for the files they contain. In many cases, adjusting the plugin load order is enough to resolve these conflicts, however, sometimes a more specific exception may be required. The section below covers both scenarios.
- The easiest way to resolve these conflicts is to adjust plugin load order so the preferred mod loads after the conflicting plugin, following the manual sorting steps in the previous section.
- If the plugin cannot be moved due to master dependencies, intentional plugin record ordering, or other constraints, the alternative is to extract the necessary files from the archive so they are treated as loose files. Loose files follow mod priority rules and override files contained within BSAs. This can be done by following the steps below. Some steps containing instructions already covered in this guide have been abbreviated.
- Click the Archives tab on the right pane of the main MO2 window.
- Right-click the BSA file of the mod you want to take precedence and select Extract….
- In the Extract BSA window that comes up, choose a folder to extract files to and click the Select Folder button.
- When finished, open the folder and 🗑️Delete all files and folders you do not need.
- Create a .zip file (or similar) with the remaining files and 👆Drag it into the Downloads tab on the right pane of the main MO2 window.
- Alternatively, you can create an empty mod and 👉Move the remaining files into it to save from having to create and manage another .zip file.
- 🛠️Install and ✅Enable the mod in the mod list.
- Ensure it overwrites all other loose files.
- NOTE – The above steps extract ALL files from the archive since this is the only option with built-in tools. Alternatively, you can 🛠️Install and ⚙️Configure an executable for a program like 🔗Bethesda Archive Extractor so that you can 📦Extract only the files you need instead.
¶ 4.7. Profile management
⏩️Skip to section 5 if you are already familiar with how to manage profiles in MO2, otherwise, proceed. Profiles allow you to modify your load order and experiment freely without affecting your primary setup. If something goes wrong, you can easily switch back to your original settings. Note that profiles do not duplicate the mods themselves, they reference the same installed mods but allow different configurations.
🔥ADVISORY – In Mod Organizer 2, hidden files (.mohidden) are shared across all profiles. This means that file-specific exceptions made for one setup will also apply to all other profiles. To manage files differently between profiles, you must create a separate copy of the mod so its files can be handled independently.
- Your currently selected profile is displayed in the profile dropdown at the top left of the left pane in the main MO2 window.
- To switch to a different profile, click the dropdown and select another entry in the list.
- Alternatively, when managing profiles, you can select a profile from the list and then click the Select button to enable it.
- To manage profiles, click the dropdown and select the <Manage…> entry in the list.
- Alternatively, you can click the Configure profiles icon in the main application toolbar.
- The following options are available when managing profiles:
- With a profile selected from the list, you can perform many simple actions, like renaming, removing, or updating profile-specific settings.
- To create a new profile, click the Create button to start from scratch, or Copy to use an existing profile as a base.
- NOTE – New profiles created from scratch will not have any mods enabled.
- The ☑️ Use profile-specific Save Games option allows the selected profile to use its own separate set of save files. Save games from other profiles will not appear in-game.
- The ☑️ Use profile-specific Game INI files option uses separate 📄Skyrim.ini, 📄SkyrimPrefs.ini, and 📄SkyrimCustom.ini files for this profile so that configuration changes can be made without affecting other profiles.
- When creating a new profile, configuration files are copied from the currently active profile—These are not empty files or reset to default.
- To change this behavior, select the ☑️ Default Game INI Settings option during creation to use a fresh, default game INI file.
- NOTE – When the ☑️ Use profile-specific Game INI files is enabled, all INI modifications MUST be made via either the INI Editor or by selecting the Open INIs folder option from the folder icon at the top right of the mod list. Profile-specific INI files are stored within the profile and loaded through MO2's virtual file system, meaning they are not written to the 📁Documents folder until the game is launched. Editing the INI files in this location will not affect the active profile. The latter option is shown below.
¶ 5. Additional notes
This section covers additional behaviors and considerations that are useful to understand when working with modded setups, including both general modding concepts and tool specific information which doesn't fit in the other sections of this guide.
- Skyrim has limits on how many plugins can be loaded. Full plugins (ESM and ESP) have 254 usable slots, with 2 of the 256 total slots reserved internally. Light plugins (ESL and ESL-flagged ESPs) use a separate pool that was increased from 2048 to 4096 in version 1.6.1130. For Skyrim VR users, this light plugin limit is also supported as long as 🔗Skyrim VR ESL Support is installed.
- Mod Organizer 2 uses a Virtual File System (VFS) to manage files. Unlike Vortex, MO2 does not move, link or otherwise deploy files directly into the game folders. Instead, all mod files remain in the staging folder at all times. When an executable is launched through MO2, the final 📁[🐉Data] folder is assembled virtually on the fly based on mod priority and presented to the game or tool as if it were the real folder. Once the executable closes, the VFS is removed. This means the game folder itself is never modified and remains in a true vanilla state. For this reason, all external tools must also be added and launched through MO2. If launched normally, they will only see the physical 📁[🐉Data] folder, which does not contain any managed files.
- By default, Mod Organizer 2 can only manage files in the Skyrim 📁[🐉Data] folder. This behavior can be extended to the root 📁[🐉Skyrim] game folder as well using the 🔗Root Builder plugin for MO2.
- With regard to INI overrides provided by mods through matching 📄PluginName.ini files, only certain INI settings can be overridden. Values that are evaluated at runtime may be affected, but settings that are only read when the game starts are applied before plugins are loaded and cannot be changed afterward. For example, grass settings are often safe to override this way, while most video settings are not.
- MO2's integration of LOOT will provide helpful flags and messages in the plugin list about plugins in your load order, such as when cleaning is recommended, etc. This topic is outside the scope of this guide. For more information on cleaning files, see my guide on 🔗How to Clean Skyrim Game Files.
- Record conflicts between mods do not merge automatically. If multiple plugins modify the same records, the one that loads last takes precedence, and any overwritten records from earlier plugins are ignored unless a patch is used.
- Required masters only define the minimum requirements for plugin placement and do not reflect all record-level conflicts. Identifying and resolving these conflicts to achieve your intended setup may require more careful review of a mod's stated recommended load order, a tool like xEdit, and even custom patches, which are beyond the scope of this guide.
¶ 6. Changelog
See below for a full revision history of this guide (↕️Expand the 🗒️Full Changelog block).
🗒️Full Changelog: (↕️Expand for details)
- Version 1.0.1 (03/07/2026)
- Added Wrench and Folder buttons to key elements in section 4.1 (Main interface overview)
- Version 1.0.0 (02/25/2026)
- Initial release
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