Pizza Tower shifted from a puzzle/exploration-based game to a fast-paced game during development in response to videos of people speedrunning the SAGE 2019 demo.

Two of Peppino's sprite animations are references to non-verbal Italian gestures:
• One of his idle animations has him bite his hands, a threatening (and sometimes sexually loaded) gesture known as "si t’ancagliu" or "when I catch you, I'll kill you".
• The pose he does on the P-rank screen is "l'ombrello" or "the umbrella", an Italian equivalent to the middle finger.

When one defeats Spoiler:The Doise, The Noise's exclusive boss fight, he is Spoiler:killed by what appears to be a fake version of Peddito. If one rematches the Doise on the hub world, The Noise will simply find his bloody corpse and look on in confusion. Fitting with this joke, in the final boss, the Doise does not have a phase in the boss rush, instead just having his corpse thrown on the ground by Pizzaface, giving the player some time to breathe, then disappearing.

"Meatophobia", the ominous background music that plays when approaching Pillar John and activating Pizza Time, features a timestretched version of the same hip-hop orchestral hit sample used in the Small Graffiti sound effect from Jet Set Radio.

Pizza Tower first saw attention with the demo released in the fan-run Sonic Amateur Game Expo (SAGE) 2018. To coincide with the expo being themed around Sonic the Hedgehog, a temporary joke character named "Snick the Porcupine" was added, with a backstory detailing how Peppino (dressed in blue like Sonic) had intended to go to SAGE, but ended up at the "Snick Amateur Games Expo" and instead made do with Snick's games (Pizza Tower levels). Upon clearing the SAGE demo, Snick will then turn into "Snick.EXE", a parody of the Sonic.EXE creepypasta, starting an exclusive mode called "The Snick Challenge" where Peppino must evade Snick.EXE while playing through all 3 stages in the demo in order. The completion reward is a fully playable Snick with a unique moveset and animations, with taunts referencing a set of YouTube Poop music videos by user iteachvader that were based on the animated series Adventures of Sonic the Hedgehog.

Snick would later make a cameo in the SAGE 2020 demo for Antonball Deluxe - a game with connections to Pizza Tower - bringing back the same setting, playable Snick, and The Snick Challenge, but with Snick.EXE instead chasing the player through the regular demo playthrough and the requirement to collect "Ruckus Rubies" to unlock Snick. Since Snick was also not meant to appear in the final release, the Ruckus Rubies use directly-ripped sound effects from the Sonic series.

Despite his removal, Snick still makes many cameos in the final version of Pizza Tower. The tiles for the Slum hub area feature a Missing poster inquiring about Snick's whereabouts, the Refridgerator-Refridgerator-Freezerator stage features a similar Wanted poster on the side of a milk carton, one of Gustavo and Brick's taunts has Brick turn into Snick, and the Pizzaboy's Wash N' Clean area has Snick covered in a freshly-washed blanket, making him appear like a ghost. Peppino's blue outfit also returned under the name "Sage Blue", which can be unlocked by clearing Floor 1 in less than an hour.

According to programmer Sertif in a reply to a now-deleted tweet, Gustavo's steed Brick the rat is intended to be female. Composer ClascyJitto corroborated this and assumed that the reason fans did not know this beforehand was because it was not overtly stated in the game.