Run Windows Apps on Linux With Steam Proton: Non-Steam Setup, Limits and Bottles Comparison

What Steam and Proton actually are​

Valve's own repository describes Proton as a compatibility layer based on Wine. Valve's wording is "a compatibility tool for Steam Play based on Wine and additional components", and its stated purpose is Windows games. It makes no promise about general-purpose desktop software. That framing matters for everything below.

Proton is not simply "Wine, but better". It is a Wine-based package with Valve's patches, bundled components such as DXVK and vkd3d-proton, and tight Steam integration. Wine and Proton have separate development processes. Valve's public changelog shows the two exchange work. Older entries note that hundreds of Proton patches were upstreamed or became unnecessary after a Wine rebase. The changelog also shows Proton fixes arriving on its own schedule and mostly targeting games.

The Bottles documentation makes a similar point from the other side. It says Valve collaborates on Wine's development and that many features built into Proton are also in recent Wine versions. Bottles recommends the Proton runner mainly where a specific game needs one of its patches. So Proton may help or may not, depending on the app.

What's new: Steam is making this easier​

Valve's October 7 Steam client beta changes the first step of the workflow below. The release notes state that "Windows binaries registered as non-steam games will now run in Proton by default." Before this, a Windows executable added as a shortcut did not route through Proton automatically, and users had to set a compatibility tool manually under the shortcut's Properties.

Three limits apply:

• The update went to Valve's Preview/Beta channel, so the stable client isn't affected yet.
• No date has been given for the change to reach the stable Steam client, and the beta remains opt-in.
• The notes don't say whether the default covers shortcuts created before the update or only new ones.

On the stable client, assume you still need to pick the compatibility tool yourself. Even with the beta default, you can change it.

The workflow, step by step​

This is the procedure the XDA author describes. It is one writer's method, not an official Valve walkthrough.

1. Install Steam on your Linux PC. Download the Windows application's installer first.
2. Add the installer to Steam. Choose Games, then Add a Non-Steam Game to My Library, and select the installer executable.
3. Choose the compatibility tool. Open the entry's Properties and go to Compatibility. Tick the option to force a specific Steam Play compatibility tool and pick one. The author says Proton Experimental is a sensible first try. You can also pick stable Proton, older releases, community Proton forks, or the Steam Linux Runtime. The older "Legacy" runtime is a separate choice and needs testing.
4. Run the installer through Steam. Let the installation finish.
5. Find the installed program. Steam keeps pointing at the installer, so the new executable has to be located by hand. The author says to look in the compatdata folder under the Steam library, typically ~/.local/share/Steam/steamapps/compatdata/. Folders there carry numeric IDs, not app names. Inside the right one, go to pfx/drive_c and then Program Files or Program Files (x86).
6. Repoint the shortcut. Open the entry's Properties again. Paste the full path of the installed executable into Target. Paste its containing folder into Start in. The entry should then launch the real app.

Caveats on that procedure​

• Paths vary. The compatdata path above assumes a default, native Steam install. Flatpak installs and extra Steam library drives can use different locations. Check your active Steam library rather than assuming.
• "Newest folder" is a guess. The author suggests opening the most recent folder. That works if you have only just installed the app. It is unreliable if other prefixes were touched recently. Check the folder contents before you edit anything.
• Clean-up needs care. The author says you can remove an app from Steam and delete its folder to wipe its Windows data. Removing the shortcut and deleting files are two separate actions. Delete the wrong prefix and you lose that program's data. Confirm which folder belongs to which entry and back up anything you care about first. The source doesn't say where saves or settings live.
• Isolation needs checking. The author says each added app gets its own Windows filesystem. That matches how Proton normally keeps one prefix per Steam entry. Confirm it on your own setup, because the source gives no tested distribution or client version.

Steam versus Bottles​

Bottles' documentation describes it as built around selectable runners. These include Wine runners such as Caffe, Lutris and Vaniglia, plus Proton and Proton-GE. It offers Application, Gaming and Custom environments with adjustable preferences and dependencies. Steam has fewer controls. You get per-entry tool selection and a prefix per entry, and you can install helper software into the same prefix. You don't get Bottles' dependency installers or its deeper configuration.

The XDA author reaches the same conclusion. Steam is less flexible than Bottles but convenient because many people already use it.

What the author's tests show​

These are firsthand results from the author, not independently verified compatibility data.

• Worked: Notepad++ ran about as well as the author could hope. Vivaldi, which has a native Linux build, launched. Its webcam worked in a Discord call, though the author couldn't see other participants' video while others could see them.
• Failed: Clip Studio Paint installed but crashed on launch. OBSBOT Center ran until a webcam was connected, then crashed. Microsoft 365 wouldn't install. The author says Wine behaves the same way for all three.
• Affinity: The installer wouldn't launch under Steam. It does run under Wine, but the app then fails. The author got it working only through a dedicated Affinity-on-Linux project, and calls it finicky even then.
• Runtime switching helped: Under Proton, Vivaldi and OnlyOffice showed a KDE window frame rendering around the app and breaking the UI. Switching to the Legacy Steam Runtime fixed it. The author describes the result as behaving like Wine.

The pattern is the point. Simple, self-contained apps are the best candidates. Apps that need hardware access, complex installers, licensing components or heavy dependencies are risky. Changing the compatibility tool can fix some problems, but it won't fix everything.

Practical takeaways​

• Prefer native builds. If an app has a Linux version, use that.
• Test your exact app. Desktop environment, Proton version and hardware all affect results.
• Change one variable at a time. Try Proton Experimental, then stable Proton, then another runtime.
• Know when to switch tools. If Steam fails, Bottles, plain Wine or a project dedicated to that app may do better.
• Treat Microsoft 365 as a known problem. The author's attempt to install it failed.

Bottom line​

The headline claim is stronger than the evidence. Steam plus Proton is a handy, low-friction way to run some Windows apps on Linux, and Valve's beta is removing one manual step. It isn't a better Wine for everything, and Valve describes Proton as a tool for games. If your target app is simple and has no Linux version, adding it as a non-Steam game is a reasonable first test. Just be careful about which folder you delete afterwards.