Stardew Valley and Minecraft modder reporting in with no issues. In general, anything Steam is moddable without issues.

It would be weird for a mod to break compatibility of a game unless it’s a DLL hack

Anything that’s steam workshop should just work for the most part.

There’s also steam tinker launcher which you can use as a shim between steam and your proton in order to hook modloaders like modorganizer for Skyrim.

Anything that’s “drag and drop” should also work seamlessly.

Worst case scenario you can add your mod organizer as a non-steam game and browse to your game folder in the mod tool.

Same as far as I can tell. I installed model swap mods for several games, workshop mods for binding of isaac and terraria, and did other random things to games like tweak configs and shit. All of it worked fine. The biggest issues I had is installing random old games in my collection to my steam deck that weren’t on steam already, and even that I still managed to make it work.

Cyberpunk 2077 mods work great from Nexus Mods. World of Warcraft mods work great from Curseforge.

For most games I’m sure you can find a way to do it. If you use protontricks you are able to run an exe under a proton prefix for a game (basically a virtual windows drive in a folder for the game) which I’ve had pretty decent luck with.

If you play games that support mod organizer 2, there is a sh install script somewhere for support in proton/steam that works well (I can find if you like), but the program does run pretty slow and is fairly buggy. Usable with patience. Upside is it can run MO2 for a given game direct from steam if configured correctly

I was able to add a couple of mods that I created myself to Rimworld just fine.

It varies but generally if there is a will there is a way. Sometimes it just works, sometimes intervention required.

Typical things that may or may not be needed depending on game:

Windows packages and/or Dll overrides via launch arguments or winecfg/protontrick

Separate wine prefix with specific weird wine build to run mod managers or editors etc. with links to relevant directories in game prefix

Case insensitivity which can be set per directory on empty directories on ext4 (poorly made mods only usually)

Searching “[game name] mods [steam deck or linux]”

Regretting all of that to find that there is a Linux mod loader that works 100% but google stopped giving meaningful search results decades ago and the reddit trick doesn’t work as well post api-suicide.

My son does tmodloader via steam, but I think its native Linux. Works without issue.

I play WoW and run Trade Skill Master (in the same wine bottle prefix). I also run RaiderIO/WoW Up/CurseForge (Linux native).

I had issues with mods for The Forest and Sons of the Forest. Never got them working.

FF XIV DPS meter worked after a lot of tinkering. Had to go to a specific discord to get the info as the modders didn’t keep their READMEs in GitHub up to date. Wish that shit was searchable.

So, it’s a mixed bag in my experience…

For terraria tmodloader works no issue, I think forge has a native client for WoW, and Minecraft is linux native anyway EDIT: I only ever modded terraria and minecraft so idk about any more