The physical inputs for Sonic Adventure 2: Battle vary from platform to platform; however, the in-game controls remain the same. The player controls their character from a third person perspective, and can run in all directions, usually via a joystick, as well as the ability to jump on all characters. The camera can usually be rotated with a few additional buttons, and depending on which character is being controlled (and which gamemode is being played), more controls are available. For instance, Sonic has the ability to roll, spin dash, homing attack, and more.

The game also features Chaos Controls, which is the ability for a character to warp from one location to another, either instantly or at incredibly fast speeds. Interestingly, the only time this ability can be used outside of a cutscene and while the player has control is during the two-player footrace mode, where Shadow the Hedgehog uses Chaos Control to freeze time (from his perspective) and get ahead in the race.