There are 39 Bronze Trophies, 3 Silver Trophies, 4 Gold Trophies, and 1 Platinum Trophy.
| Unlockable: | How to unlock: |
| ...This Is Now (Bronze) | Set off the explosives in the present. |
| 15-Hitter (Bronze) | Perform a 15-hit combo. |
| 25-Hitter (Bronze) | Perform a 25-hit combo. |
| 35-Hitter (Silver) | Perform a 35-hit combo. |
| Battle Bloxx (Bronze) | Defeat 50 enemies as Bloxx. |
| Branching Out (Bronze) | Defeat 50 enemies as Wildvine. |
| Building Bloxx (Bronze) | Unlock Bloxx. |
| Cannon Fodder (Bronze) | Defeat 50 enemies as Cannonbolt. |
| Codon Collector (Gold) | Collect all Codon Crystal power-ups. |
| Constructive Feedback (Bronze) | Unlock Feedback. |
| Diamond In The Rough (Bronze) | Defeat 50 enemies as Diamondhead. |
| Extreme Earth Makeover (Bronze) | Discover the morphic generator. |
| Feedback Frenzy (Bronze) | Defeat 50 enemies as Feedback. |
| Focused Destruction (Bronze) | Destroy 8 crates in a single attack. |
| Four Times The Fun (Bronze) | Defeat 50 enemies as Four Arms. |
| Future Malformed (Bronze) | Defeat Mucillator. |
| Goin' Mutts (Bronze) | Defeat 50 enemies as Wild Mutt. |
| Gravattacktics (Bronze) | Defeat 50 enemies as Gravattack. |
| Have A Ball (Bronze) | Unlock Cannonbolt. |
| Heated Exchange (Bronze) | Defeat 50 enemies as Heatblast. |
| Heavy Duty (Bronze) | Unlock Gravattack. |
| Human Power (Bronze) | Defeat 20 enemies as Young Ben or Teen Ben (not in alien form). |
| It's Hero Time (Bronze) | Complete the entire game on Hero difficulty. |
| Just Chillin' (Bronze) | Defeat 50 enemies as Arctiguana. |
| Look, Grandpa--No Aliens! (Silver) | Defeat 50 enemies as Young Ben or Teen Ben (not in alien form). |
| Mass Destruction (Gold) | Destroy 150 crates in the game. |
| Muttin' To It (Bronze) | Unlock Wildmutt. |
| Not A Scratch (Bronze) | Complete an entire level without being defeated and reset. |
| Omni What? (Bronze) | Defeat 30 enemies as Young Ben or Teen Ben (not in alien form). |
| Omnitrix To The Max (Gold) | Fully upgrade all of Ben's alien forms. |
| Omniverse Overlord (Platinum) | Earn every Trophy in the game |
| Open Season (Bronze) | Open 75 Tech Repositories over the course of the game. |
| Past Due (Bronze) | Defeat the Queen Ant and rescue Grandpa Max. |
| Plumb Crazy (Bronze) | Lure Malware into the Plumber Training Room. |
| Plumber Power (Silver) | Fully upgrade all of Rook's Proto-Tool functions. |
| Shockingly Effective (Bronze) | Defeat 50 enemies as Shocksquatch. |
| Smoothie Operator (Gold) | Collect all Smoothie power-ups. |
| Super Cool (Bronze) | Unlock Arctiguana. |
| Technical Difficulties (Bronze) | Take out Psyphon and rescue Blukic and Driba. |
| That Was Then... (Bronze) | Plant the explosives in the past. |
| The Eyes Have It (Bronze) | Defeat 50 enemies as Eye Guy. |
| The Galvanic Butterfly Effect (Bronze) | Escape from Malware... for now. |
| Think Fast (Bronze) | Defeat 50 enemies as XLR8. |
| Training Time (Bronze) | Completed the training simulation... and wrecked the timeline. |
| Two Malwares... No Waiting (Bronze) | Defeat both Malwares and fix the timeline. |
| Up In The Air (Bronze) | Defeat 30 enemies while they are in the air. |
| Weird Scientist (Bronze) | Steal Animo's tech and lure Malware to the cavern. |
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