The Super Game Boy is compatible with the same cartridges as the original Game Boy: original Game Boy cartridges, the Game Boy Camera, and dual-mode Game Boy Color cartridges (in Game Boy-mode). The unit could map the four shades of green to various colors on the screen. Later Game Boy games that were optimized to use the Super Game Boy had additional color information and could override the on-screen colors, display a graphical border around the screen, and display special background sprites, as seen in the Mario's Picross title screen. Those games would have printed a small "Super Game Boy Game Pak" logo on the box and cartridge. The adaptor could support up to 64 colors for the border, and 12 colors for the screen. Static screens could display all 10 colors.[3] Certain games can load multiple borders depending on the player's location in the game, such as Dragon Warrior I & II.[4]

It is also possible for Super Game Boy games to make use of the Super NES hardware for extra effects, as demonstrated in Contra: The Alien Wars, Donkey Kong, Kirby's Dream Land 2, A Bug's Life, FIFA 98: Road to World Cup, Madden '97, Animaniacs and Toy Story; these games had expanded sound when used with the Super Game Boy. Wario Blast, the Game Boy version of Primal Rage, the Game Boy version of Killer Instinct and several other titles even allowed the second Super NES controller to be used for two-player action. The title screen changed to show that these games had a two-player option, rather than a connection status. Using the Super Multitap, some games even supported four players. The original Super Game Boy does not support game link multiplayer because, according to a Nintendo spokesman, a two-player configuration would interfere with the RF signal from the television.[5]

The Game Boy version of Space Invaders allowed players to access a Super NES version of the game as well as a colored version of the Game Boy game. The SNES version is copied into and run from the SNES's internal 256KiB work RAM.

Some black Game Boy Color cartridge games also have Super Game Boy enhancements, although there isn't any logo indicating this on the cartridge or on the front of the box as there are for original Game Boy releases. Several GBC titles do have a small Super Game Boy compatibility icon located on the back of their packaging, such as for Dragon Warrior Monsters 2: Cobi's Journey.[6]