The Super Game Boy was compatible with the original monochrome Game Boy cartridges and black Game Boy/Game Boy Color cartridges, although it would display the latter in monochrome. The unit could map the four shades of grey to various colors on the TV. Later Game Boy games which were optimized to use the Super Game Boy had additional color information, and the ability to display a graphical border around the screen. Those games would contain a small "Super Game Boy Game Pak" logo on the box and cartridge. The adaptor could support up to 64 colors for the border (4 palettes of 16 colors each), and 16 colors for the screen (4 palettes of 4 colors each). Since the background color is shared among all 8 palettes, the number of colors is actually 61 for the border, and 13 colors for the screen. Colorization was applied to the screen itself, and did not scroll with the background. While static screens could display all 13 colors, actual in-game graphics used fewer. Usually the colors were divided such that a large scrolling area with moving sprites was assigned one 4-color palette, and a non-moving status bar was assigned the remaining palettes.

It was also possible for Super Game Boy games to make use of the SNES hardware for extra effects. For example, Asteroids/Missile Command and Donkey Kong (among others) had expanded sound when used with the Super Game Boy. Wario Blast, the Game Boy version of Killer Instinct, and several other titles even allowed the second SNES controller to be read as another player, and the title screen changed to show that it had a two-player option, rather than just "connect." In the most skillful use, Space Invaders allowed players to play a full 16-bit version of the game that took over the entire screen.

No version of the Super Game Boy is capable of running games that are designed strictly for the Game Boy Color, although they will run dual mode (black cartridge, compatible with both systems) games in Game Boy mode. Some black cartridge games also have Super Game Boy enhancements, although there is no logo indicating this on the cartridge; however, a less prominent logo appears on the back of the packaging, downplaying Super Game Boy's compatibility in favor of the newer Game Boy Color.