WarioWare, Inc.: Mega Microgame$! (and by extension, the WarioWare sub-series as a whole) evolved out of the Sound Bomber mode in Mario Artist: Polygon Studio, which pitted the player in various rapid-fire minigames incorporating their 3D models. Several developers at Nintendo R&D1 grew fond of the mode and decided to flesh it out into a full game. According to Yoshio Sakamoto in a 2006 interview, the decision to rebrand it as a Wario spinoff came about because "we couldn't think of anyone else who would be best for the role. Wario is always doing stupid things and is really idiotic, so we thought him and the rest of the characters would be best for the game." The project was initially worked on in secret, but was immediately (albeit flatly) greenlit once the developers revealed it to their manager.

As a remnant of this inspiration, the microgames "Crazy Cars", "Diamond Dig", "Repellion", "Wario Whirled", "Batter Up", "Mario Paint: Fly Swatter", "Hectic Highway", "Racing 112", and "Maze Daze" are all directly based on Sound Bomber's minigames. Additionally, the boombox interstitial that appears between microgames in certain modes is a modified version of the one from Sound Bomber.