The Noise, Pepperman, and The Vigilante were all planned to be playable at some point - Vigilante and Noise were both intended to be regular playable characters, while Pepperman was intended as a one-level only character on Refrigerator-Refrigerador-Freezerator, much like Gustavo & Brick. All 3 of them have code and animations left over in the game, of varying compatability. The Noise would later be re-added in a future update due to all of his animations being completed.

The Captain Goblin on the Crust Cove level originally was called Captain Bomb and had a more humanoid design. The only animations made for him are simply the same image rotated and modified.

Pizzahead's third phase was originally going to be, instead of a boss rush, Pizzahead growing desperate and starting to violently attack Peppino directly through kicks and punches rather than cartoon gags. This was scrapped as the development team didn't want Pizzahead to be perceived as an angry character as much as just an evil clown.

The Weenie and Burger Golfer enemies are based on Peter and Mac, the protagonists of an unmade Pizza Tower predecessor called Weenie Cop.

Many fans and critics have noted similarities between the aesthetic of Pizza Tower and "off-model" 1990s cartoons such as Ed, Edd, n' Eddy and The Ren & Stimpy Show. Game creator McPig has claimed not to be a fan of those series and to have not been influenced by them, although he did still take influence from the more cleanly-drawn SpongeBob SquarePants, and an unclear inspiration from 1990s cartoons would still be cited on the game's Steam store page description.

One of the enemies in Pizza Tower, the Pickle, is based on the Roper enemy from the game Memoirs of Magic, with modifications to more closely resemble a pickle as to fit the game's food theme. On the "Oh, Shit!" level, graffiti can be seen of a Pickle with a muscular arm bearing a tattoo reading "MOM", which has a double-meaning as both a reference to a stereotypical tattoo and an acronym for its origin game's name.