Sonic Origins marked the first time that Sonic the Hedgehog 3 and Sonic & Knuckles were re-released since 2011. It has been speculated, but not outright confirmed, that this prolonged release was due to complications involving the ownership of the original soundtrack, which was made in part by musicians Michael Jackson and Brad Buxer. It was later announced that the Origins version of the games would replace the original soundtrack with rearranged versions of songs from the games' first PC port, Sonic & Knuckles Collection, that were written without Jackson's involvement. These versions were rearranged by series composer Jun Senoue.

Sonic Origins contains leftover data from the then-unreleased Sonic Frontiers. This is how it was first discovered that Big the Cat and his fishing minigame would return in Frontiers.