Existing tutorials for Steam Deck modding use weird setups that often don't work, or require different installation instructions. You can simply run ModEngine2 through Steam, which lets you use the same installation steps as Windows PC users, and doesn't remove your ability play the unmodded vanilla game.
You'll need to be in desktop mode if you're not already.
Setup
1 - Download the latest version of ModEngine2 from this link. Right click the ZIP file in your downloads folder, and choose "extract archive here". Right click the extracted file modengine2_launcher.exe and choose "Add to Steam".

2 - Go to the properties window for modengine2_launcher.exe in your Steam library.

3 - Change the launch options to -t er -c config_eldenring.toml as shown below:

4 - In the Compatibility tab, force the use of Proton as shown below (I don't think the version matters, but I chose Proton Experimental):

Running mods
After following this, you can install ModEngine2 mods the same as on Windows PCs. Add mod files to the mod folder, or add DLLs to external_dlls in config_eldenring.toml. Mod descriptions usually explain which one to do.
To launch the game with mods, play modengine2_launcher.exe from your Steam library. To launch the game without mods, play ELDEN RING from your Steam library.
Notes
Unless the mod author says to, do not:
- ❌ Use a different ModEngnine2 build from the one linked here
- ❌ Replace or modify any files in your ELDEN RING/Game folder
- ❌ Change the Steam launch options for ELDEN RING
- ❌ Install anything that claims to be an "anti-cheat toggler", "mod loader", or "mod launcher" other than ModEngine2
Installing mods in unusual ways will make it hard to find help online, and may remove your ability to play the vanilla game.
Note that ModEngine2 will use a separate save file location ~/.local/share/Steam/steamapps/compatdata/<appid>/pfx/drive_c/users/steamuser/Application Data/EldenRing/<steamid>/ER0000.sl2. The appid is 1245620 for vanilla, and a random number for modded. You can copy files between these locations to transfer saves.
7 comments
Unfortunately, I also didn't get it working, after I run the modengine2_launcher.exe with that launch option, there is a console flashed then nothing happened.
But I did find an alternative way, which I guess is exactly what the author means by "Installing mods in unusual ways will make it hard to find help online, and may remove your ability to play the vanilla game.".
Please try with caution and I don't know if it works for you or if you will get banned.
This is mentioned in ModEngine-2.1.0.0-win64/README.txt as a less recommended way, but it did work for me.
I just simply downloaded the ModEngine2.1.0.0 from the link provided in this guide, and installed the mod like PC way, and I put the ModEngine contents directly into the elden ring Game/ directory, and I renamed the modengine2_launcher.exe into start_protected_game.exe so steam will automatically launch it when I start the game in library (original eldenring in steam).
sadly, i followed everything carefully, and when I launch the .exe, it doesn't work...what am I doing wrong ?