- For a brief second in the Columbia Pictures logo, the Torch Lady turns into Jane Fonda as Cat Ballou. This is taken directly from that film's Logo Joke. And for an even briefer second (three non-sequential frames to be exact), the logo shifts to the Logo Joke from Cloudy with a Chance of Meatballs, with the Torch Lady getting knocked off her pedestal by a giant banana.
- As the Super-Collider is destroying itself, the FLDSMDFR from Cloudy with a Chance of Meatballs can be seen.
- Miles's room includes a poster of the album cover from Chance the Rapper's Coloring Book, except Chance's hat now says "4" instead of "3" on it.
- The license plate number on Jefferson's police car is "RFD 690", which is a common New York prop plate number appearing in various media, the most notable example being the lead detectives' car in Law & Order.
- The creators have outright stated that Peni's animation and design was particularly inspired by the Sailor Moon anime.
- Peter Porker's animation and design looks reminiscent of the Looney Tunes. He also looks similar to Porky Pig. Even lampshaded when the Spiders return to their home dimensions. Porker's parting words are "That's all, folks!", prompting an immediate reply from Peter: "Can he say that? You know, legally?"
- In the background of Gwen's reality in her focus trailer is a poster advertising Clone College, with Abe and JFK in similar positions to the poster for 22 Jump Street.
- Some billboards seen in Times Square include a Shaun of the Dead sequel called "From Dusk Till Shaun", which was what the creators of the original film said a potential sequel would be called.
- Another billboard is advertising Hi, Hello, a riff on the actual ''Oh, Hello" show starring Nick Kroll and John Mulaney (who also voices Spider-Ham in this film).
- Yet another billboard advertises a film called "Baby Shower" which seems to be that universe's Bridesmaids (or possibly a sequel to that movie).
- The Weeknd's "Starboy" cover appears as an ad in Miles' version of time Times Square (albeit with his old haircut) and it also takes the name of his first album "Kissland" (spelled KISSLND in this universe) while in universe the album is released under The Weeknd's real name, Abel Tesfaye.
- Aaron has Community on his TV, specifically a scene from "Anthropology 101" where Troy gets out of bed in a Spider-man shirt. Donald Glover who plays Troy was partly the inspiration for Miles Morales, voiced him in past adaptations, and played Aaron in Spider-Man: Homecoming.
- The Spider-Lair is obviously modeled on the Batcave from the DC Animated Universe down to the display array of multiple Spider-Man costumes with blue lighting illuminating them.
- During the ending, Miles zips past a store called "Perry Joe", a reference to Joe Perry, lead guitarist of Aerosmith and noted Spider-Man fan who performed the theme song for Spider-Man: The Animated Series.
- The number 42 appears throughout the movie. According to the director, it's a reference to Jackie Robinson's jersey number. It's also directly lifted from Miles' origin story, where both the lottery ball that earns him a scholarship to Brooklyn Visions, and the spider that eventually bites him and gives him his powers, are both conspicuously marked "42".
- As Peter B. Parker shouts at Miles to "push the green button", a PlayStation controller appears with its topmost face button highlighted green. The same button (triangle) is indeed colored that on the real controller.
- In Miles' version of Times Square, there's an image of Stephen Curry, the professional basketball player.
- Doc Ock cuts a tree down the center then rips it apart, similar to how Doctor Octopus rips a table in half during the bank robbery scene in Spider-Man 2.
- After the collider causes some lampposts to turn into what looks like bizarrely colorful artpieces, some pedestrians look at one of them while someone remarks "I think it's a Banksy".
Shout Out / Spider-Man: Into the Spider-Verse