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The original was posted on /r/steamdeck by /u/theclosedeye on 2025-06-01 11:06:40+00:00.
Prefixes are located in "/home/deck/.steam/steam/steamapps/compatdata" (ty, u/phil_davis, for correcting me) folder.
I play a lot of GoG and Uplay games and recently I decided to clean up old prefixes. It was an instant +10 Gb of free space.
Each non-steam game (that uses proton) you add occupies anywhere from 0.5 to 1.5 Gb, so don't forget to delete it's prefix folder, after you no longer need it. Remember, however that this is where your saves are stored, so back it up somewhere.