The size of Metroid Prime's save data is under ~60 bytes in size. According to programmer Zoid Kirsch, the reason why the save data is so tiny is because each room in the game has a set of "world layers" that define which objects spawn when the room is loaded (e.g. world layers change Flaahgra's room from having a boss to Chozo Ghosts and an Artifact when returning later). World layers are also used for items like Energy Tanks or Missile Expansions; when they are picked up, they are on a separate world layer that is disabled once the item is acquired. If that layer wasn't disabled, the item would be there the next time the room is loaded.

A world layer state is represented by a single bit in the save data, and since there are only a few hundred world layers in the whole game, it ends up requiring just under ~50 bytes to represent them all, with the remaining bytes in the save data representing health, missile count, etc. When Nintendo asked Retro Studios how many memory card blocks Metroid Prime was expected to take up, Kirsch said: "One!" A GameCube memory card block is 8 KB, which was much more space than needed to save the game.