During the run-up to the game's release, SoBe aided the promotion by giving away a number of Oddworld-themed decorated goods, and Oddworld Inhabitants were able to return the favour by replacing a number of Health Up Vendos in the North American version with SoBe vending machines that function the same way. However, this led to a number of fans thinking that Oddworld Inhabitants had sold out and refused to ever have any association with Oddworld ever again, resulting in them being removed entirely from the PAL versions of Munch's Oddysee. This removal even applied to all the re-releases of the game except for the PC and Switch versions, where the SoBe vending machines are retained in some of the levels.

The Possession Orb used for Abe's possession ability was added as a solution to handle the ability in a 3D environment. An earlier idea was to have Abe automatically target the closest possessable character the player could see, similar to the earlier Oddworld games, but this was later scrapped.

The Intern's at Vykker's Labs have 5 "fingers", and no thumbs. Their vertical mouths were stitched together completely in order to prevent them from whistling to the sound of their annoying music.

Abe's Mother, Queen Sam, was meant to have a role in the game but due to time constraints, this particular part of the plot was cut.

Munch's Oddysee was originally going to be released for the PlayStation 2, with different level layouts, enemies, cutscenes, and areas, but was scrapped and put on the Xbox.

The idea to move the game to Xbox was based on the development team not only wanting to use a more powerful console, which would allow them to flesh out the world better, but also thinking it would be a better long term plan to publish the games on the console. Microsoft even worked with Oddworld Inhabitants to help make the Xbox better for them to work on it.