TMNT saves your progression, scores, upgrades, and options. Each time you complete a level, buy an upgrade, make a new high score, or change an option, the game will save, showing either the screen or icon shown above. If a level is left before reaching the result screen, neither progression nor energy shards collected will be saved.

The game offers three different save slots that allow starting and saving different progressions. There is no way to directly erase them but they can be overwritten.