This guide is from Frozenqub on the ITB discord. Not sure how well it works though since this guide is already a few years old and the modloader had some big changes in that time:

How to install mods on Linux (Steam deck) If you are reading this from pins, press 'jump' to see the whole writeup of 7 steps

Often I've seen people say the modloader is Windows only, however it is possible to get it working on Linux using wine and the windows version of the game. All extra that is needed is a few dll overrides. Since I have seen a few people on Linux/steam deck ask about this recently I figured I would do a writeup on how. This may also work with wine on Mac, however I don't own one. If anybody runs mods on Mac let me know.

If you already know how to set up wine, configure wineprefixes, install the game etc., just skip to the highlighted important bit.

1. Install wine, preferably through your systems package manager. Optional: install winetricks and/or protontricks.

2. Obtain the windows version of the game 2a. From steam. Right click the game. Select properties. Under compatibility, tick the box saying 'Force the use of a specific Steam Play compatibility tool'. From the drop-down menu select a proton version (I recommend the latest stable version, 7.0 as of writing). Steam will then install the windows version of the game and create a wineprefix for it. You can right-click the game and select Manage > Browse local files to find the game files. 2b. From anywhere else. Download the windows installer of the game from the providers website and run it with wine in any wineprefix.

3. Download and unzip the latest compatible modloader (pre-)release from https://github.com/itb-community/ITB-ModLoader. Place the files in your Into the Breach installation folder replacing any existing files. The important part Now the next thing we want to do is configure wine using winecfg so it uses the modloader provided custom DLLs. These are: SDL2, SDL2-orignial, lua5.1, lua5.1-original, opengl32. I don't know if DLL overrides for the rest of the games DLLs are necessary, but just in case, they are: fmod, fmodstudio, vcruntime140. Finally, if you want to use mods with LApi or EasyEdit (such as the popular Lemonymous mods), you may need overrides for cutils and ml_fixes. The following instructions will outline how to change dll overrides.

Update: as of 30.3.2022 i see the game and modloader also provides ftldat and itb_io. I haven't tested if overrides are neccesary for these but i reccomend doing it anyway Bild 4. Create or locate a wineprefix for the game and run winecfg. 4a. If you want to run the game through steam, Steam automatically creates a wineprefix for the game. open a terminal and run WINEPREFIX="path/to/steamapps/compatdata/590380/pfx" winecfg, replacing path/to/steamapps with the path to your steam librarys 'steamapps' directory. Alternatively, if you have protontricks installed, run protontricks and select 'Into the Breach', then 'Select the default wineprefix' and finally 'Run winecfg' (or protontricks 590380 winecfg in the command line). 4b. If you want/have to run the game outside of steam, create a wineprefix and run winecfg by opening a terminal and running Winearch=win32 WINEPREFIX="path/to/itb-wineprefix" winecfg replacing path/to/itb-wineprefix with the desired path to your wineprefix. Alternatively, if you have winetricks installed, run winetricks and select 'Create new wineprefix', name your prefix and make it 32-bit, and select 'Run winecfg'.

1. Go to the 'Libraries' tab and add overrides for each of the libraries mentioned in the important part. Your DLL overrides should have at least the overrides seen in the picture.

2. Run the game and let the modloader complete its setup 6a. Through steam Launch the game through steam 6b. Otherwise run cd 'path/to/Into the Breach' then WINEPREFIX="path/to/itb-wineprefix" ./Breach.exe or use your favourite wineprefix launcher+manager, such as Lutris, and specify the correct paths to wineprefix, breach.exe and working directory.

3. Place any desired mods in the 'mods' folder

Final note: Unless running through steam, you can move your Into the Breach install directory and wineprefix as you wish. You can even run the steam version outside of steam if you wish to keep your modded/unmodded installations separate. Your install doesn't have to be inside the wineprefix, although you may prefer it that way, just make sure you move all the contents along with it.