How to Manage Save Files and Mods on Steam Deck
The Steam Deck is a powerful handheld gaming PC, but its Linux‑based OS and Proton compatibility layer can make file management a little confusing. Locating save files, installing mods, and transferring data between your Deck and a desktop PC isn’t always straightforward. Whether you’re trying to skip a lengthy intro, keep save files safe when uninstalling a game, or get a batch file mod to work, this guide covers everything you need to know about managing game files and saves on the Steam Deck.
We’ll explore where things live on the internal drive, how to work with Proton prefixes, and the best ways to back up and restore your progress. By the end, you’ll be able to navigate the Deck’s file system like a pro and solve common headaches with missing saves or mod installations.
Navigating the Steam Deck File System
The Steam Deck’s operating system (SteamOS 3) is based on Arch Linux, so files are structured differently than on Windows. Understanding the main locations for game and save data is the first step toward taking full control of your library.
Where Game Files Are Stored
Steam games you install through the normal library end up in the SteamApps folder. The default path is:
/home/deck/.local/share/Steam/steamapps/common/Each game gets its own subfolder here, named after the game’s internal identifier (for example, Oblivion might be under oblivion). You’ll also find the ACF files that track installation status in the steamapps folder above.
If you’ve added an SD card, Steam can create a separate library there. The path will be something like /run/media/mmcblk0p1/steamapps/common/. The rest of the folder structure mirrors the internal drive.
Where Save Files Are Stored
Save file locations depend on whether a game runs natively on Linux or through Proton. Native Linux titles usually store saves inside your home directory (often in ~/.local/share/ or ~/.config/) following the XDG Base Directory Specification. For these, cloud saves via Steam should work seamlessly.
Proton‑powered Windows games, however, store their save data inside a Wine prefix. Each game gets its own prefix folder under:
/home/deck/.local/share/Steam/steamapps/compatdata/[AppID]/pfx/The [AppID] is the unique numeric identifier for that game on Steam. Inside the pfx folder is a miniature Windows environment, complete with a drive_c/ that mimics the classic C: structure. This is where you’ll find the same directories a game would use on a Windows PC (Documents, Saved Games, AppData, etc.). The exact subfolder varies by title, so you’ll often need to look for the developer’s name or the game’s name.
Locating Your Save Files
Finding a specific game’s save folder can seem daunting because of the AppID system, but there are reliable methods to pinpoint the right spot.
Using the Steam App ID to Find Prefixes
Every game on Steam has a unique numeric App ID. You can find it by visiting the game’s store page (the ID is in the URL) or by using a site like SteamDB. Once you have the number, navigate to compatdata/[AppID] to access that game’s Proton prefix. From there, you can browse the virtual Windows drive to locate saves.
For example, The Elder Scrolls IV: Oblivion has the AppID 22330. Its save folder is typically at:
/home/deck/.local/share/Steam/steamapps/compatdata/22330/pfx/drive_c/users/steamuser/Documents/My Games/Oblivion/SavesIf a game uses a different location (like AppData), consult the PCGamingWiki page for that title. It lists the Windows save path, which you can then map into the prefix’s drive_c tree.
Example: Oblivion Saves
Oblivion’s save location is known, so you can quickly access it using the file manager (Dolphin) on the Deck. Enable “Show Hidden Files” in the hamburger menu, then follow the path above. Once there, you’ll see .ess save files that you can copy, delete, or replace as needed.
Managing Save Files
Knowing where your saves live is only half the battle. Here’s how to use that knowledge for backup, transfer, and advanced save management tricks.
Backing Up and Transferring Saves
The simplest way to protect your progress is to copy the entire save folder to a safe location (like an SD card or cloud storage). On the deck, you can use Dolphin’s split view (F3) to copy files from the prefix to a backup folder. Even though many games support Steam Cloud, it may not trigger correctly for every title, so having a manual backup is wise.
To transfer saves from a PC, first locate the save folder on your Windows machine, then copy those files to the corresponding prefix directory on the Steam Deck (or vice versa). For games that use Steam Cloud, your saves should sync automatically when both machines are online, but a manual copy acts as insurance.
Playing with Multiple Save Files for Different Paths
Some games limit you to a single play-through, but you can manage multiple parallel saves by creating separate folder copies. For instance, rename the original save folder to Saves_Rogue and create a fresh folder named Saves for a new playstyle. When you want to switch, swap the folder names. This technique works best for titles that don’t bind saves to a Steam account or cloud sync, so consider turning off cloud saves for that game first.
Skipping Game Intros Using Save Files
Many players want to bypass lengthy introductory sequences. If you download a 100% completion save or one that starts after the intro, you can place those save files in the proper folder. As with the multi‑path method, you may need to rename them to match the game’s naming convention (e.g., Save001.sav). Always back up your current saves before overwriting anything. Online communities often share save files for games like Final Fantasy XVI that allow you to jump straight into the action.
Installing Mods on Steam Deck
Modding a game on the Deck follows the same principles as on a Windows PC, but you’ll be working inside the Proton prefix. Most mods that require file replacements simply need to be copied to the correct folder. Mod managers like Vortex or MO2 can be set up through Proton, but manual installation is often easier.
Accessing Mod Folders
The game’s installation directory is inside steamapps/common/, while any config files the game generates live in the Proton prefix. Some mods go directly into the game folder (texture packs, DLL injectors), while others modify files in the “Documents” area of the prefix. Use the same compatdata path to reach the virtual Documents and AppData folders.
Running .bat Files (Windows Batch Scripts)
Mod installers for older games, like the Final Fantasy XIII HD mod, often come as .bat files, which are Windows batch scripts. These won’t run directly on Linux, but you can execute them inside the game’s Proton prefix using Protontricks.
First, install Protontricks from the Discover store (the graphical interface for Winetricks/Proton). Then, open a terminal (Konsole) and use a command like:
protontricks -c "cmd" 292030Replace 292030 with your game’s AppID. This launches a Windows command prompt within that prefix. From there, navigate to the folder where your .bat file is (using DOS cd commands) and run it by typing its name. If the batch file expects certain drive mappings, you may need to map folders to drive letters with the subst command inside the prompt. As an alternative, you can open the .bat in a text editor, see exactly which files it copies or moves, and perform those steps manually using the Steam Deck’s file manager. That avoids any command‑line hassle altogether.
Troubleshooting Missing Files After Proton Installation
One of the most common frustrations happens when you install a game with Proton and can’t find your saves, or you reinstall and everything seems to have vanished. Here’s why and what to do.
When Steam creates a new Proton prefix for a game, it assigns a dedicated compatdata folder using the AppID. If you change the Proton version in the game’s compatibility settings, Steam might create a completely new prefix instead of reusing the old one. This doesn’t delete your previous saves; they’re still in the original folder. To restore them, navigate to compatdata, find the folder for that AppID (it might have a timestamp suffix or a temporary name if the old one was moved), and copy the save data from the old pfx into the new one.
When you uninstall a game through Steam, the game’s files in steamapps/common/ are deleted, but the compatdata/[AppID] folder typically remains intact. That means your saves and other user data survive an uninstall by default. However, if you choose to “Delete Proton Prefix” in the Steam client’s developer options, you will permanently delete that folder. Always make a backup before using that option.
For games that rely on third‑party launchers or DRM, save locations can become even more obscured. If you still can’t find them, use the find command (e.g., find ~/.local/share/Steam/steamapps/compatdata -iname "*save*") to search for likely file names within the prefixes.
Frequently Asked Questions
How can I run .bat files on my Steam Deck for mod installation?
You can run a Windows .bat file inside the game’s Proton prefix using Protontricks. Launch a terminal and use the command protontricks -c "cmd" AppID (replace AppID with the game’s numeric ID). This opens a Windows command prompt. Navigate to the batch file’s location and execute it. Alternatively, read the .bat contents and manually perform the file copy/move operations using the Steam Deck’s file manager.
Do save files get deleted when uninstalling games on Steam Deck?
Generally no. Uninstalling a game removes the game files from steamapps/common/ but leaves the Proton prefix folder (compatdata/[AppID]) intact. Your saves remain safe. The only exception is if you explicitly delete the Proton prefix through the Steam developer settings.
My FFXVI save files are missing, what should I do?
First, check if you recently changed the Proton version. A new prefix may have been created, leaving your saves in the old folder. Browse compatdata for the FFXVI AppID (look for a folder named with that number) and check both the current and any renamed copies. If you reinstalled the game, the prefix may have been regenerated; copy your saves from the backup (or the old prefix) into the new one.
How can I skip game intros by using save files?
Download a save file that starts after the intro sequence. Locate the correct save directory for the game (inside its Proton prefix or native save folder) and place the downloaded file there. Rename it to match the game’s expected save name if necessary. Make sure to back up your own saves first.
Can I play with multiple save files for different paths in the same game?
Yes. In the game’s save folder, create separate subfolders or rename the main save folder to keep multiple sets of save files. When you want to switch paths, swap the folder names so the game reads from the correct set. Disable Steam Cloud syncing for that title to prevent accidental overwrites.
Where do I store my game save files on Linux?
On Linux, native games usually place saves in ~/.local/share/, ~/.config/, or occasionally in a hidden folder right in your home directory. For Proton/Wine games, saves are inside the respective prefix folder under /home/deck/.local/share/Steam/steamapps/compatdata/[AppID]/pfx/drive_c/. The exact subdirectory depends on the game (Documents, Saved Games, AppData, etc.).
How to access game files and mod folders on Steam Deck?
Use the Dolphin file manager and navigate to /home/deck/.local/share/Steam/steamapps/common/ for the game’s installation directory. For mods that need to be placed in the user folder (like Documents), go through compatdata/[AppID]/pfx/drive_c/users/steamuser/. Toggle “Show Hidden Files” in Dolphin to see the .local and .steam folders.
Can’t find files after installing a game with Proton, why?
After a fresh installation, the Proton prefix is created the first time you launch the game. If you looked before running the game, the prefix might not exist yet. Additionally, if you switched Proton versions, the old prefix could be renamed. Check the compatdata folder for any folders with the same AppID and a timestamp suffix. Also ensure you’re looking in the right “users” folder inside the prefix; sometimes Steam creates the user as “steamuser” or the actual Linux username.
Where can I find my save game files for Oblivion?
On Steam Deck, Oblivion saves are at /home/deck/.local/share/Steam/steamapps/compatdata/22330/pfx/drive_c/users/steamuser/Documents/My Games/Oblivion/Saves. If you don’t see them, ensure the game has been launched at least once and that hidden files are visible in the file manager.
