If any installed mods contain save data that must be kept between runs for example, custom unlockables then this would be a big concern, as deleting the mod's save data would remove this progress. It is recommended to avoid continuing any saved games if any mods are enabled. This could be due to the mod author not knowing how to enable this, or the mod's data being too complicated to save. Many mods do not or cannot retain save data in a continued game. While introducing official modding support, mods for this game are infamous for not working properly due to how the API was constructed and the lack of suitable, comprehensible documentation. To enable unlocking achievements with mods enabled, you need to defeat Mom at least once with all of your mods disabled. Mods that do not use the Steam Workshop can be installed by downloading them and extracting them to the appropriate location. The game must be started to install the mod into the game. Mods found in the Steam Workshop can be installed by navigating to the mod's page and clicking Subscribe. Mods can typically be found in the Steam Workshop or various community sources.

Mods can be installed in a few different ways, depending on how the author chose to share it.

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