Steps:
1. Open Options tab in cookie clicker.
2. Scroll down to the Mods section and select Manage Mods.
3. Click Open /mods folder.
4. Open the Workshop folder.
5. Open the folder for the mod you want to enable achievements on.
6. Open the info.txt file.
7. Copy "AllowSteamAchievs": 1, and paste it under the Disabled line near the bottom.
8. Save the text document.
9. Restart game.
Achievements should now be enabled for that mod, repeat for any other mods that are messing with achievements.
Source: https://steamcommunity.com/sharedfiles/filedetails/?id=3231496781
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