Each of the games can be upscaled to high-definition (720p), and the graphics can be de-pixelated through the use of an optional screen filter. Each game is given three savestates which allows players to save at any point in the game and restart from that point later. In addition there are options to adjust the volume levels of the game sound, music, and sound effects. Each standard game has a museum section which contains game info, trivia, and cartridge and game case images.
There are also unlockable games and interviews with the original game developers. The Xbox 360 version includes achievements and the PlayStation 3 version includes trophies.
Disappointingly, the lock-on feature of Sonic & Knuckles is not included in any version, and thus Sonic 3 & Knuckles, Knuckles in Sonic 2, and Blue Sphere are not in the game. Sega Mega Drive Ultimate Collections producer, Ethan Einhorn, stated that in order for those games to be included, the other unlockable games would have had to be dropped in order to have enough time to get the lock-on feature working.
Like Sega Mega Drive Collection before it, the game contains a number of unlockables that were released on other home consoles and arcade platforms.