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Hello, @DYuQeYMCVK0L

Here is the some key points which will help you.

Games installed via the Itch.io app typically store their saves in a directory within the app's data folder. This location can vary depending on the operating system:

Windows: The saves are often stored in a directory within the %APPDATA%\itch\apps folder.

macOS: Saves may be located in a directory within the ~/Library/Application Support/itch/apps folder.

Linux: Saves can be found in a directory within the ~/.config/itch/apps folder.

You can check the specific location by navigating to the game's installation directory within the Itch.io app and examining the file structure. Once you identify the location, you can configure your Game Save Manager to back up saves from that directory.

I hope this info will help you.
Best Regard,
geraldine198

Games installed via the Itch.io app typically store their saves in a directory within the app's data folder.

English is not very precise here. Which app do you talk about?

Because, well, the itch app and the installed games do not care either way. Itch is not Steam. The app only downloads the stuff for you, there is no "install" in most cases. It is unzip and run. It does not matter if the app does this, or if you do this with your browser. 

Especially with renpy games. All renpy games I know, are "portable". They do not care, where the executeable is. They will save their save game in two locations. That user folder in appdata and the game folder as a backup.