Dr. Robotnik's Mean Bean Machine is a modified reskin of the Japan-exclusive Sega Mega Drive version of Puyo Puyo. The first training levels of Puyo Puyo were removed from Dr. Robotnik's Mean Bean Machine, but they can be put back in through hacking. If this is done, the Puyo Puyo characters Skeleton T., Nasu Grave, and Mummy are replaced by a character that has the intro of Coconuts with the mugshot of Scratch.

The game has a sound test menu that is only accessible if played on a Japanese Mega Drive. However, the game was a Western release only, so the only way to access this is with a hacked system that bypasses the region lockout.

This is the first Sonic game to be based on a cartoon, as all the opponents are from Adventures of Sonic the Hedgehog.

Although Dr. Robotnik's Mean Bean Machine was not released in Japan during the Sega Mega Drive's lifespan, it would receive its first Japanese release in 2000 for Windows as part of Sega Archives from U.S.A. Vol. 2, the Japanese version of Sega Puzzle Pack.