- Each level is themed around movies.
- Kamoshidaman takes cues from Superman, where Kamoshidaman is depicted as a hero.
- Junessic Land is very heavily themed around Jurassic Park, with dinosaurs roaming a jungle. The In-Universe inspiration for Junessic Land, as well as the movie itself, involved talking dinosaur children working together to survive in reference to The Land Before Time.
- A.I.G.I.S has a logo that references A.I.: Artificial Intelligence, while the concept of the level references I, Robot.
- The fourth labyrinth is based on animated musicals such as The Wizard of Oz and Snow White and the Seven Dwarfs, as well as a biopic.
- A.I.G.I.S' central plot features a world rebuilt by an A.I. godhead after a series of wars caused by humans with personality, eventually ending with what seems to be an ICBM strike. This is clearly referencing how the Millenium Kingdom came into being in Shin Megami Tensei I, which nearly happened in the Persona universe but was averted, causing the the Persona series Alternate Timeline.
- Hikari's secondary school trauma (Which created Junessic Land) features a nearly identical synopsis as "Bacterial Contamination" by Daijoubu P, which also features students trying to isolate a bullied student in fear of getting bullied themselves, as the bullies will attack anyone who makes friends with the bullied. Of course, this simply fuels the bullied student's depression further.
- The Theater District is a direct reference to Etrian Odyssey, as it is basically a massive tree akin to the Yggdrasil seen in the series; The Cinema street's floor are branches that flows movies into the cinemas, and the projectors at the bottom are its roots. Much like the trees polluting themselves over time and spill back the pollution into the world, the films in the cinema street only fuel emotional poison into the Cinemas, where the people trapped watch them and get more depressed than they already are.
- While choosing code names for Yukiko, one option is to call her "Black Fire". Combine this with her Ultimate Persona, Amaterasu, does this sound familiar?
- In the background of Theodore's shop is a mannequin wearing a red-and-green striped sweater and a hockey mask.
- References to cinema abound in the weapon flavor text including The Great Escape, Lawrence of Arabia, Indiana Jones, Star Wars, and much, much more.
- One of the intros to Elizabeth's special screenings begins with her stating "Next time on Dragonba...". Futaba catches the reference and even quotes the "over 9000" meme.
- Another DBZ reference shows up later, after the special screening to get the Joker/Yu Unison Attack. Yu responds to a comment that his friendship level with Joker is "over 9000", channeling Frieza and boasting that it's 530,000.
- In true Etrian Odyssey style Schmuck Bait, one Ticket has you finding a nice relaxing clearing and Teddie suggesting the group take a nap there. Agreeing with him will get you attacked by butterfly Shadows with devastating poison attacks. Futaba comments after the fight that it was a pretty obvious ambush that you usually see in video games.
- The ticket description for Quest 22 "Learning from the Bad Guy" contains the line, "Tell it to take its stinkin' paws off you."
- One of the "bad words" that Futaba taught Aigis is "Saradaba!" This is actually a Japanese meme that came from Fist of the North Star which is a misheard phrase when Shin attempts to finish Kenshirou that is used as a slang term for a self-destruct move in a fighting game.
- When Yu and Joker first encounter each other in Junessic Land, their skirmish is almost the same as the Vicious/Spike sword versus handgun fight in Cowboy Bebop - even ending in the same pose!
Shout Out / Persona Q2: New Cinema Labyrinth