The DS version of Bolt is different from the main console and PC version. It is also a 3D action game and just like the other version, it does not follow the events of the movie but instead focuses on the fictional TV series that is set inside the film. The player needs to complete different missions for the show, controlling Bolt (who gets the main focus) and/or Penny. The TV series focuses on the evil character Mr. Calico who has kidnapped Penny's dad and attempts to destroy Earth with missiles. The game is played on the bottom screen and the top screen shows the name of the current mission, elapsed time and mission progress. The game is played in 3D, but generally there is always a linear progression to the right, while characters can move around in any direction in the environment during fights. Characters have a health bar and a separate bar for powers. The DS version uses on-screen text and no voice acting unlike the other version.

Bolt uses attacks and different superpowers such as a sonic bark to attack. Penny has a Wheelbar to fight and she can also use it to zip along edges and scale buildings. By beating opponents, it is possible to collect energy bits that are used to level up and access improved abilities and new combos by spending them in three areas: damage, armor, and energy expense (Bolt)/Wheelbar speed (Penny). Characters attack and jump using buttons and the touch screen is used for special attacks, which are unique to each character. Bolt's other powers such as laser vision and super strength are only used for solving minor environment-based puzzles. When using laser vision, objects can be pierced in specific locations by tracing an outline on the touch screen. There are also platforming sections, but the game does not let characters fall off ledges, and jumps can only be performed when lined up correctly. Every now and then, a boss needs to be defeated, and optionally, enemies can be skipped to complete levels.

The game supports multiplayer in two different modes. One of them is a hacking minigame also present in the single-player part. Using the touch screen, players use the stylus to complete patterns by linking numbers and shapes as they appear in the top screen, building up a meter within a time limit. In multiplayer, both players can disturb each other's game using power-ups. The second multiplayer mode is a subgame similar to Super Monkey Ball, where players use the D-pad or touch screen to tilt the level and roll sidekick character Rhino through mazes, avoiding five types of obstacles. It isn't possible to fall off the stage in this minigame either.

The game includes the chatroom device tool DGamer. After registering on the website, players can use a Wi-Fi connection to log in and enter different Disney-related chatrooms to talk to other players. It includes a profile system with an avatar that can be customized. Additional features are unlocked gradually by progressing through the game.