Hello guys! I've been struggling with modding SKSE on Linux forever. I've tried Vortex and Lutris, but neither of those have worked for me. Eventually, I switched to using ModOrganizer2 and protontricks which worked. Here's what worked for me:

Skyrim & Proton Setup

1. Install Steam (I used a system package manager, but flatpak should be fine too. For the rest of my guide, I have the steam directory as ~/.local/share/Steam. If you use Flatpak, the directory will be different, so you may need to symlink the flatpak directory to ~/.local/share/Steam for things to work)
2. Install Skyrim SE from Steam, go into the configuration and make sure it uses Proton Experimental as the compatability layer.
3. Launch Skyrim SE once to generate proton prefixes.

Install Protontricks

I tried using protontricks from APT, but it wasn't working, so I recommend using the flatpak version of protontricks. I used this command:

flatpak install com.github.Matoking.protontricks 

Protontricks allows you to interact with Skyrim's proton prefix (Steam/.../489830/pfx/) in a clean way using the Wine dialogs. :)

install the Windows version of Mod Organizer 2

1. Download a MO2 .exe file from the GitHub.
2. Install it in Skyrim's proton prefix using protontricks:
   • Make sure you've run Skyrim once
   • Launch Protontricks
   • Select Skyrim Special Edition → default wineprefix
   • Choose “Run an arbitrary executable” and select your downloaded MO2 installer wherever it is

Locate MO2 Executable

After installation, the main executable will usually be:

C:\Modding\MO2\ModOrganizer.exe 

This means that every time you want to install/edit mods, you should launch this .exe with protontricks.

On Linux, the corresponding path is:

~/.local/share/Steam/steamapps/compatdata/489830/pfx/drive_c/Modding/MO2/ModOrganizer.exe 

Create a Desktop Launcher for MO2

In order to make it easier to launch MO2 without launching protontricks and pressing a bunch of buttons and finding the file, you can make a desktop entry, which will appear directly as an app on your computer.

Create a .desktop file in ~/.local/share/applications to launch MO2 conveniently:

[Desktop Entry] Name=Mod Organizer 2 (Skyrim SE) Comment=Launch Mod Organizer 2 in Skyrim Proton Prefix Exec=flatpak run --command=protontricks-launch com.github.Matoking.protontricks --appid 489830 "/home/{USERNAME}/.local/share/Steam/steamapps/compatdata/489830/pfx/drive_c/Modding/MO2/ModOrganizer.exe" Icon=/home/{USERNAME}/.local/share/icons/modorganizer2.png Terminal=false Type=Application Categories=Game;Utility; StartupWMClass=ModOrganizer.exe 

• MAKE SURE YOU REPLACE {USERNAME} with your Linux username
• I also included the Icon=/home/{USERNAME}/.local/share/icons/modorganizer2.png line so that the app has an icon. This isn't required but it gives the app a nice icon. See below on how to extract the icon.

You may have to make the desktop entry executable:

chmod +x ~/.local/share/applications/modorganizer2-skyrim.desktop 

Extract MO2 Icon

To give your desktop entry a nice icon, You can extract the icon from the MO2 executable using 7zip:

7z x ~/.local/share/Steam/steamapps/compatdata/489830/pfx/drive_c/Modding/MO2/ModOrganizer.exe ".rsrc/ICON" -o./extracted_icons 

• Save the extracted PNG (the highest quality is #10) to ~/.local/share/icons/modorganizer2.png
• Update the .desktop file to point to this path

MO2 + Nexus

Mod Organizer asked me to connect Nexus when I launched it, so it should work seamlessly with Nexus mods website.

yay!