According to STI director Roger Hector, Michael Jackson was initially brought in during development to compose music for the game, even though no mention of his involvement was included in any of the game's credits. This was supposedly due to the scandals that arose around Jackson at the time. His involvement was removed from the title, and much reworking, including all the started music, had to be done.

In December 2009, Michael Jackson's composer Bradley Buxer (credited in Sonic 3 as Brad Buxer) told French magazine Black & White that Jackson was actually involved with some of Sonic 3's compositions, supposedly not being credited because he wasn't happy with how they sounded, due to the lack of optimal sound reproduction on the Genesis.