- When the Investigation Team first appears in the Persona 3 path, they're all doing the signature poses of major characters from JoJo's Bizarre Adventure.
- One conversation that comes up between Chie and Yosuke about the fourth stratum explicitly mentions Inception's "dream within a dream" meme.
- In one quest, Teddie imbibes a love potion and falls in love with Akhiko. One of the lines he says while Akihiko is trying to flee is "YOU'RE BEARING ME APART, AKKY!"
- This homage to Star Wars:Ken: "Will eating meat gum make me taller?"Junpei: "Don't be seduced by the meat side!"Chie: "Join meat, and together we can rule the galaxy!"
- In one conversation, Rise speaks of the "plight of the navigator."
- After crafting "Mystery Food X: The Final Edition", Naoto says that "It's a weapon that's surpassed all my expectations".
Shout Out / Persona Q: Shadow of the Labyrinth