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While FunKey S autosave save files (''.quicksave'') are entirely incompatible with external emulators, FunKey S emulator save state files (''.000'', ''.001'', etc.) other than those of the PlayStation are compatible with matching emulators on other platforms, such as the PC version of FCEUX in the case of NES games. Additionally, for games that support them, the transfer of in-game saves is an alternative option that is generally compatible with a wider range of emulators. Note, however, that a third-party emulator having an in-game save file format with a matching file extension does not guarantee that it will be listed below, as other factors, such as expected save file size, can impact in-game save file format compatibility between emulators. As battery-based in-game saving did not become commonplace until the 1990s, games for earlier systems emulated by the FunKey S, such as the Nintendo Entertainment System, Master System, TurboGrafx-16, and Sega Genesis, often do not support this type of saving, with many, such as all Atari Lynx games with an in-game save feature, using password-based saves instead. WhenFor aseveral gamedozen doesNES supportand battery-basedGenesis in-game savinggames, however, an[[List in-gameof saverecommended fileROM ishacks#SRAM generatedhacks|SRAM forROM ithacks]] thecan firstbe time it attemptsused to save data, with the extension of this file depending on the system the game is for. A table containing the correspondingadd in-game savesaving fileto extensiongames forthat eachdid officiallynot emulatedoriginally systemhave with in-game save file supportit, asoften wellreplacing asmore thetedious storage locations of these files and the thirdpassword-partybased emulators compatible with them, is listedsaving belowsystems.

Transferring an in-game save file onto or off of the FunKey S is done by simply moving the file in question into or out of the folder in which in-game saves are stored for that game's system; usually the same folder as the game itself. Note that PlayStation ''MCD'' files, placed in the ''memcards'' folder within the PlayStation folder of the FunKey S, should be named ''card#.mcd'', with the hashtag symbol replaced by the first number starting from one that isn't already used by an existing ''MCD'' file. In regards to SNES save files, if you don't see the ''.snes96_snapshots'' folder in your computer's filesystem, its Unix-based operating system is hiding hidden folders. {{HiddenFolderExplanation}} Note that as in-game save files generated by the Mednafen emulator include a string of characters between the game name and file extension, such save files must be renamed to remove the string of characters (ex. ''.9d599a43d2c69738f3562f58aeff8828'') before they can be detected by emulators other than Mednafen. For the FunKey S, this applies to the TurboGrafx-16, Game Gear, Neo Geo Pocket, and WonderSwan systems. If you find that a third-party emulator compatible with any in-game saves generated by the [[#Which emulators does the FunKey S use?|emulators of the FunKey S]] is not listed below, feel free to add it yourself or inform a wiki editor.