If a cheat device is detected, Mitsuru and Fuuka will chastise the player for cheating during battles, voice acted.

The final boss, Spoiler:Nyx, is female. Nyx's avatar, Ryoji Mochizuki, is male, however when scanned by Fuuka, she will scan and talk with female pronouns.

Trish, the Fairy from previous Persona games, makes a cameo appearance in Persona 3 as the host of a TV show called "Who's' Who" in which she interviews characters from past games.

The persona Alice, a reference to Lewis Carroll's "Alice in Wonderland", has a signature move called "Die For Me!" in the North America release. This was changed from the Japanese version's name of "Could you die for me?".

Shinjiro Aragaki's persona, Castor, and Akihiko Sanada's persona, Polydeuces, are twins. Spoiler:This foreshadows how they are connected and also which of the two would die during the game. The orginal Greek myth that serves as the origin of their names depicts Castor dying and Polydeuces living on.

There's a video game the protagonist receives called "Innocent Sin Online", a fictional MMORPG. Playing it will merit you the S. Link of the Hermit with a character who's screen name is "Maya". The name Maya is the name of one of the main characters in "Persona 2: Innocent Sin", as well as the protagonist in the follow up game "Persona 2: Eternal Punishment". The protagonist also has the screen name of "Tatsuya", referencing the protagonist of "Innocent Sin".

Cielo, the blue haired protagonist with dreadlocks from the Digital Devil series, has a soda named after him. Named Cielo Mist, it is described as being from Jamaica, giving reference to the American portrayal of him having a Jamaican accent.

All the blocks' names in Tartarus, with the exception of the optional basement, Monad, are taken from the seven worlds of the Quabalah.

In the PS2 update, Persona 3: FES, in the chapter "The Answer", all levels of the Abyss of Time get their names from Dante's "The Divine Comedy":
• The First Door, Malebolge, is the level where people who commit fraud are punished.
• The Second Door, Cocytus, is the lowest level of hell divided into for regions (the next four) where people who commit the sin of betrayal are punished.
• The Third Door, Caina, named after the Bible's Cain, is where people who betrayed family dwell.
• The Fourth Door, Antenora, named after Antenor from Homer's "The Iliad", is where people who betrayed their country dwell.
• The Fifth Door, Ptolomea, named after Ptolemy, governor of Jericho from the Bible who killed his guests, is where people who betrayed guests dwell.
• The Sixth Door, Judecca, named after Judas Iscariot also from the Bible, is where people who betray masters or benefactors dwell.
• The Seventh Door, Empyrean, is named after the the highest level of Heaven.

While Cerberus is Koromaru's persona, a version of Cerberus can also be used by the game's Protagonist through the use of a cheat device.

Koromaru is likely based off a real dog named Hachikou. Both dogs owners died, but the dogs go to the place they last saw their master, to wait for them to return.

Concept art shows that Ken originally used darts as a weapon, not spears as in the final game.

During one of the anime cut scenes, Ken's red armband on his sleeve will disappear and reappear at the end of the scene.

Junpei's original victory pose alludes to John Travolta's disco pose from the movie "Saturday Night Fever".

According to Aram Jabbari, Assistant Manager of Public Relations and Sales, Persona 3's "M" rating in the United States is due to cultural differences between Japan and the USA.

Takaya Sakaki's gun is a Smith & Wesson Model 500, according to the Persona 3 concept art book.

In the opening for Persona 3 FES, the protagonist, Junpei Iori, Yukari Takeba, and Akihiko Sanada are seen approaching the Full Moon Hermit boss. Spoiler:However, this isn't possible in the game, as Junpei Iori is captured by Chidori Yoshino before that mission, and could not be a part of your party for that fight.

A set of early development videos show that there were plans for battles to be conducted through a fluid transition in the game's field, rather than in a designated battle area. Enemies would rise from the ground as a battle began, rather than causing a screen transition.

It was originally intended for Persona 3 Portable to include a "good" ending for the female protagonist involving Junpei confessing his love for her like the other male teammates. This was scrapped from the finalized version, however, the data remains in the game's data, including Junpei's Japanese voice files.

The intro song to Persona 3 FES is actually a remix of two different songs; The song "Memories of You" (the credits theme) and the song "Burn My Dread" (The main theme of Persona 3).