Secret Sly Masks are a new collectible in Thieves in Time and are floating insignias similar to the lives found in Sly Cooper and the Thievius Raccoonus. Collecting all 60 will unlock cosmetic changes that can be toggled on and off for your characters, which are listed below. There are a total 60 masks hidden throughout the game, but they can also be hidden in stages and mini-games, unlike with Clue Bottles, which are only hidden throughout the hubs. There will be no indication of where the masks are, except actually being spotted by the player.
| MASKS | UNLOCK | WHAT IT DOES |
| 5 | Monkey Glider | A Paraglider skin |
| 10 | Camo Glider | A Paraglider skin |
| 15 | Ultimate Sly | New skin for Sly |
| 20 | Ultimate Bentley | New skin for Bentley |
| 30 | Ultimate Murray | New skin for Murray |
| 40 | Ultimate Carmelita | New skin for Carmelita |
| 50 | Ratchet's Wrench | Changes Sly's cane to Ratchet's wrench; coins also turn into bolts |
| 60 | Cole's Amp | Changes Sly's cane to Cole's amp from Infamous 2 |
