The Game Boy Micro is compatible with all Game Boy Advance cartridges, including Game Boy Advance Video cartridges. Unlike the Game Boy Advance and Game Boy Advance SP, however, the Game Boy Micro does not support games made for the original Game Boy or Game Boy Color. The e-Reader card series is also officially incompatible because the accessory cannot fit, but physically removing the link cable connector from the e-Reader will make it fit. However, the design of the e-Reader makes the "Select" and "Start" buttons difficult to access during gameplay, and its size and shape in relation to the system makes it awkward to hold. Physically removing the link port connector from the e-Reader will prevent the accessory from linking up with other Game Boy Advance systems or the Nintendo GameCube due to its necessity in transferring data through the link cable.
As with the Game Boy Advance and Game Boy Advance SP systems, there are no regional lockouts on software, so North American games can be played on Japanese hardware and vice versa.