In the Japanese dub of the game, during the December 4th visit to the hospital to question Taro Namatame, he says the line: Spoiler:"Then… little by little, the image came into sharper focus." After the end of this line, you can very faintly hear a click followed by what sounds like the rustling of paper. This audio appears to be Namatame's voice actor Yasuhiro Roppongi turning the pages of his script after finishing his line read, and was accidentally left in the final game.

Chie's catchphrase, "Don't Think; Feel.", is a quote by Bruce Lee in the film "Enter the Dragon".

There is a glitch which occurs in the Western release where a random eye will appear on a persona's status screen. It was long speculated to have some hidden meaning, but it does not occur in other versions, including the PS Vita re-release, and has been stated to just be a bug by an unnamed source with special knowledge of the game's development.

The battle form of Spoiler:Mitsuo the Hero, the boss of the Void Quest dungeon, is in the style of 3D Dot Game Heroes, which was in development at the time.

One of it's attacks (Command) changes the battle command screen to that of the original Shin Megami Tensei.

Once you unlock Heaven, Spoiler: where you need to rescue Nanako from Namatame, you can go back to the Void Quest entrance to get a special message. When you try to enter the dungeon, Yosuke will say, "[player], we should be headed to find Spoiler:Nanako-chan... Our princess is in another castle, dude." This is a reference to the infamous message Toad would give Mario in the original Super Mario Bros.

On the 2nd play-through, the player can battle against Margaret. When they beat her, she will start talking about her sister Elizabeth, from Persona 3, and the boy she "took a fancy to," which is the protagonist of said game. She will also mention why Elizabeth left the Velvet Room. Spoiler:She wants to rescue the protagonist from the seal of Nyx.

During day 2 of the class trip you end up at Club Escapade. Rise says that she once had a gig canceled there because of a power outage, implying that Arcana Hermit caused it.

The Class trip takes you to Tatsumi Port Island, the main location in Persona 3. During the First Day, you go to Gekkoukan High School where you meet both Mr. Edogawa and Chihiro Fushimi.

Chihiro says she received help from last year's Class President to write her speech, implying Mitsuru Kirijo helped out.

Mr. Edogawa's lecture is important. Spoiler:It tells of the mythology behind Persona 4's last boss, Izanami-no-Okami, and the protagonist's final persona, Izanagi-no-Okami.

When you finally get to your hotel at the end of the day, you end up on Shirukawa Boulevard. The Seaside Clam-Shell Hotel is the location of Persona 3's fourth full moon shadow battle with Arcana Hierophant and Arcana Lovers.

Kanji's social link has a reference to Persona 3 Sun social link with Akinari Kamiki. In Persona 3, Akinari writes a story about a pink alligator and bird. In Persona 4, Kanji will make a pink stuffed alligator during his social link, referring to the book.

There is a Teddie weapon called Strega Claw. This is a reference to the Strega Organization, the group of Rogue persona users from Persona 3.

The fusion for Alice is a reference to the first Shin Megami Tensei for the Super Nintendo. To get her requires both Belial and Nebiros who, in the first game, she calls Uncle Red and Uncle Black.

Persona 4 has a book called "Witch Detective" that will be described by the player as:
A ploddingly-written romantic comedy about a girl on her first day of school in a new town. Vampires are involved.
... The content of this book was almost physically painful for you to read.
The summary is a reference to Stephenie Meyer's "Twilight" novel.