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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.

Tutorial source: Full video below

1: 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

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

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

2. Install Skyrim via Steam

  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. 

3. 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.

  3. 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.

This lets you run Windows-only mod tools (mod managers, script-extenders, installers, etc.) in isolation — without messing up other Wine prefixes or global configuration. The use of Bottles as the mod-tool environment (instead of the game prefix) is actually recommended by many Linux modders as of 2025. Example from community:

“Use Bottles. It is 2025. … Bottles lets you actually install dependencies like VC or .net … unlike winetricks…” Reddit

4. Use Flatseal to fix permissions, if needed

Because Steam and Bottles are running inside Flatpak sandboxes, they might not initially have permission to access your real filesystem (e.g. where Skyrim is installed, or where you store mod files). Use Flatseal to grant them access:

  1. Run Flatseal (via Flatpak).

  2. Select Steam, and grant it filesystem access to the directories where Steam installs games (and where you plan to store mods) — either via “Other files” + specific path, or broader “host” access if you don’t mind.

  3. Do the same for Bottles: grant it access to wherever you plan to store mod-tool installations, mod files, etc.

This ensures that Bottles/Wine can see your Skyrim install and mod folders correctly, and that mod tools can read/write files properly. This step is often critical to avoid subtle permission-related bugs (missing files, inability to launch, etc.). This matches the “Flatseal + Flatpak + Bottles” approach from the video. YouTube+2Steam Community+2

5. Install a mod manager inside the Bottle

Using the Bottle you created:

  • Download the Windows installer for Mod Organizer 2 (MO2) — many use an automated Linux-installer script (for example the widely used modorganizer2‑linux‑installer), but you can also manually install. Steam Community+2Nexus Mods Forums+2

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

For many users in 2024–2025, this works cleanly: one user reports running Skyrim + 230 mods in MO2 under Linux with “no more issues than … on Windows” after switching to the non-Lutris Bottle approach. Nexus Mods Forums

Once installed, configure MO2 to point to your Steam Skyrim installation (the “game folder” under Steam Flatpak).

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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