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Skyrim Mods in Linux

Prerequisites

- Linux Distro: Endeavor OS (or similar Arch-based; adjust package manager commands if needed, e.g., use `apt` on Ubuntu).
- Steam: Installed system-wide (e.g., via `sudo pacman -S steam`).
- Skyrim: Special Edition or Anniversary Edition owned on Steam. Launch it once via Steam (using Proton) to create the game prefix and download any Creation Club content.
- Internet: For downloads.
- Hardware: Standard gaming PC capable of running Skyrim. duh...

Tutorial source: Full video below

1. Install Skyrim via Steam

  • Go to https://store.steampowered.com/about/ → Download Linux (.deb).
  • Or terminal: 
  • wget -O steam.deb https://steamcdn-a.akamaihd.net/client/installer/steam.deb
    sudo apt install ./steam.deb
  • or, use flatpak in step 2.

  1. Launch Steam (Flatpak), log in. 

  2. Install Skyrim Special Edition (or original Skyrim) as usual.

  3. Once installed, run Skyrim at least once to let it create its config / prefix / compatibility files.

  4. In Steam, go to game Properties → Compatibility and enable Proton (or a compatible Proton build) to ensure the Windows version runs properly. Many mod-compatibility tools expect Windows behavior. Steam Community+1

Note: If you already have Skyrim installed: Just log in and quit. 

2. Install Flatpak and FlatHub

1. Open a terminal and update packages:  

sudo apt update
sudo apt install flatpak      # if flatpak isn’t installed already
flatpak remote-add --if-not-exists flathub https://flathub.org/repo/flathub.flatpakrepo

Then install apps:

  • If you dont have steam yet...
flatpak install -y flathub com.valvesoftware.Steam

Or, 

  • Go to https://store.steampowered.com/about/ → Download Linux (.deb).
  • Or terminal: 
  • wget -O steam.deb https://steamcdn-a.akamaihd.net/client/installer/steam.deb
    sudo apt install ./steam.deb

After installing steam (or if you already have it):

flatpak install -y flathub com.usebottles.bottles
flatpak install -y flathub com.github.tchx84.Flatseal

3. Use Flatseal to fix permissions, if needed

This gives you permissions for Bottles. 

  1. Run Flatseal (via Flatpak).
  2. In the left nav bar, choose "Flatseal"
  3. Scroll down to "All user files" and turn it on. It gives permissions for the /home directory. 
    image.png
  4. If Steam is installed in a different location, go down to "Other files" and choose were that directory is so it can have access to that. 
  5. Do the same for Bottles: grant it access to wherever you plan to store mod-tool installations, mod files, etc.

4. Create a Wine “bottle” (prefix) for modding tools via Bottles

  1. Launch Bottles.

  2. Create a new bottle: choose “Gaming”, 64-bit (for Skyrim SE), name it e.g. skyrim-mods.

It might have already done this next part for you: In that bottle, configure a runner — choose a modern Wine-based runner or a Proton-GE variant if available (Bottles often gives you that option).
                                              This provides a Windows-like environment for mod tools.

Go to hamburger menu:
  1. Preferences 
  2. In "integrations"
    1. turn on "Steam Proton Prefixes" 
  3. now completely close Bottles. OFF! X out of it!

Reopen bottles. You should see the Elders scrolls in there now... and/or all your other games that are using proton.

Choose Skyrim.  <click>

5. Install a mod manager inside the Bottle (Vortex)

Using the Bottle you created:

When downloading, it should tell you the requirements needed. Windows, dont worry about it. We do need to worry about the other one. Currently tells me ".net 6.0+" but, make sure on what it says for you first.

Go back to Bottles.

If you are not already at the right place...Click on:

  • Steam Proton: "the Elder Scrolls" or whatever your Skyrim game is named there.
  • Scroll down to Options
    • Dependencies
      • Choose "dotnetcoredesktop6" (or whatever your requirement said)

      • image.png

  • Run the installer inside the Bottle (i.e. via Bottles/Wine), so MO2 is installed in that prefix.

You should be done with that part in Bottles. Now, go back to the Nexus site and download the vortex.exe. 

Back to Bottles.

6. (Optional, but strongly recommended) Install script extenders & mod-tools inside Bottle

Many Skyrim mods rely on script extenders or Windows-only tools. For maximum mod compatibility, you may want to install:

  • Script extender (SKSE / SKSE64) — if you plan to use mods requiring it.

  • Load-order / mod-management utilities like LOOT, merge tools, mod-cleaners, ENB installers, etc.

  • Other utilities: mod merging tools, animation tools (FNIS / Nemesis), texture / mesh tools, plugin cleaners, etc.

All these should be installed inside the Bottle (Wine prefix), so they run under Windows compatibility and can access mod-folder paths properly. Many Linux-modding guides explicitly recommend using a separate prefix for tools to avoid conflicts. spacebums.co.uk+2Step Mods | Change The Game+2

7. Install mods via the mod manager, sort load order, launch

With MO2 (or Vortex) configured and SKSE / dependencies / tools installed:

  1. Add mods: either drag-and-drop mod archives (zip, 7z, rar, etc.) into MO2, or use the mod manager’s download/installation feature, depending on your preference.

  2. Activate mods, set load order.

  3. Use load-order tools (LOOT or similar) to auto-sort, then manually resolve any conflicts if needed.

  4. Launch Skyrim via MO2 (or via the Steam + Proton + SKSE launcher inside your Bottle, depending on configuration).

At this point, mods should be running as if you were on Windows.

🛠️ Common Issues & Troubleshooting Tips

Based on community reports and recent 2025 experiences:

  • Mod manager fails to detect game — Often due to Steam Flatpak’s folder structure; ensure MO2 is pointed to the correct Steam library path.

  • Permission errors / missing files — Use Flatseal to give Steam/Bottles access to the correct directories; “host” filesystem permission often solves many sandbox issues.

  • Mods with complex dependencies (SKSE, ENB, animations) misbehave — Make sure required dependencies (Visual C++ runtime, .NET if needed, correct SKSE version) are installed in the Bottle. Many Linux-modding guides highlight this. spacebums.co.uk+1

  • Performance / load-time issues — For heavily modded installs, using an SSD for game + mods improves load times significantly. This is a common recommendation in modding-on-Linux guides. spacebums.co.uk+1

  • ENB or advanced graphics mods may be finicky or unstable under Proton/Wine — ENB support on Linux remains hit-or-miss; some modders succeed, some don’t. Many guides treat ENB as “special case” and caution it may require extra tinkering.

Tutorial source:
https://www.youtube.com/watch?v=48kKsspKRiU

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