Several of the Phantom Thieves' weapons are named after real-life, religion, history, mythology and literature:

• The protagonist's Paradise Lost is named after the John Milton poem of the same name, which describes Satan's rebellion against God and the fall of man.
• Ryuji's Mjolnir is named after the mythical hammer wielded by Thor, the Norse god of thunder, while his Megido Blaster is named after Megiddo, a ruined ancient city located in northern Israel said to be the site of an end-of-days battle.
• Morgana's Claoimh Solais is named after the Irish sword of light, while his Sudarshana takes its name from the discus Chakra used as a weapon by the Hindu lord Vishnu.
• Ann's Naraka Whip and Dainaraka Whip are named after Hell in Hinduism and Buddhism; "Dainaraka" is prefixed with the Japanese word "Dai" meaning "great".
• Yusuke's Usumidori is named after the pale green sword wielded by the samurai Minamoto no Yoshitsune, while his Providence is named after the concept of divine providence.
• Makoto's Gordios is named after the Phrygian King Gordias, while the Judge End is named after the concept of the Last Judgment, where all rational creatures are evaluated at the end of days by God.
• Haru's Fleurs du Mal (French for "Flowers of Evil") is named after a volume of French poetry by Charles Baudelaire, while the Yagrush is named after a weapon crafted for the Caananite god Baal.
• Akechi's Hinokagutsuchi is named after the Shinto god of fire, who burned his own mother alive at birth, while his Ancient Days is named after the "Ancient of Days", a name for God used in the Hebrew Book of Daniel.
• Yoshizawa's Sword of Sinai is named after the biblical Mount Sinai where God gave Moses the Ten Commandments, while her Sahasrara takes its name from the Hindu Crown Chakra that controls one's pure consciousness.

Nanako Dojima from Persona 4 was considered to be added as a playable character at one point in development, sporting an older character design and an art style closer to Persona 5's art style. It's unknown why she was cut from the final product.

Fans believe Suguru Kamoshida is based off of former judo gold medalist Masato Uchishiba who spent 5 years in prison for rape and had all his medals and honors revoked.

Late in the game, it's revealed that Spoiler:Goro Akechi was the one behind the mental shutdowns and had intentions to kill the protagonist on Masayoshi Shido's orders. Spoiler:This is foreshadowed during Shujin's field trip to the television studio. Morgana tells the protagonist, Ryuji and Ann about a restaurant that serves pancakes in one of the hallways. When they meet Akechi in the same hallway, Akechi says: "Oh, am I mistaken? I thought I heard something about delicious pancakes...". This tells observant players that Akechi was able to access the Metaverse before this meeting because only those who have been there can hear Morgana speak in human tongue in the real world.

Originally, the cutscene that plays after Spoiler:the Phantom Thieves believe Ryuji to be dead after the destruction of Shindo's palace was going to feature extra lines of dialogue not present in the final game, as well as a dialogue tree for Joker, the player's character. Additionally, there are unused animations in the game's files Spoiler:showing the Phantom Thieves beating up Ryuji. In the final game, the scene cuts to black.

There were files in the games coding containing unused cutscenes where the confidants would get mad at the protagonist if he didn't visit them often enough. If he visited them after a long absence and answer the confidants' questions incorrectly, their relationship would be in doubt (as seen by an upside down tarot card) and he would lose the benefits of that social link until their relationship was repaired, similar to certain social links in Persona 3 and Persona 4. The reason this feature was removed is unknown.

When Goro Akechi Spoiler:temporarily joins the Phantom Thieves in Sae Nijima's palace, he uses the persona Robin Hood, named after the famous outlaw of English folklore. When he Spoiler:confronts the Phantom Thieves in Masayoshi Shido's palace, they have to fight him twice. In the second fight, Akechi uses the persona Loki, based on the Norse god of mischief. This marks the first Persona game since Persona 2: Eternal Punishment where someone besides the main character can use more than one persona at a time.

Almost all of the Phantom Thieves starting Personas are named after famous real or fictional outlaws or criminals.

• The protagonist's Persona is Arsene, named after the gentleman thief Arsene Lupin created by French author Maurice Leblanc.
• Ryuji's Persona is Captain Kidd, named after the Scottish pirate William Kidd.
• Ann's Persona is Carmen, named after the Gypsy Dancer seductress most notable in Bizet's opera.
• Morgana's Persona is Zorro, named after the famous Californian vigilante.
• Yusuke's Persona is Goemon, named after Goemon Ishikawa who lived during 16th century Japan.
• Makoto's Persona is Johanna, named after Pope Joan who disguised herself as a man to infiltrate the Roman Catholic clergy.
• Haru's Persona is Milady, named after Milady de Winter, the French spy from The Three Musketeers.

Futaba's Persona Necronomicon, however, isn't named after a person, but rather an object called a grimoire. This is a fictional magic textbook found in horror stories written by H.P. Lovecraft.

Goro Akechi is a reference to the character Kogoro Akechi from the Private Detective Kogoro Akechi book series by Japanese mystery writer Edogawa Ranpo.

One of the early ideas was for Morgana to be a sports car, however, he would have been too small to fit the entire gang and so the idea was scrapped.

A prototype image of the main character was drawn early in development. It was dropped after the artist, Shigenori Soejima, felt he had added too much and went for something simpler. Another early design of the main character was dropped due to Director Hashino claimed it looked "too professional". Soejima also commented that his initial changes to the design felt too cheap.

The protagonist's initial persona was going to be the German demon Mephistopheles. It was later changed to Arsene due to him fitting the theme of the game better.

Director Katsura Hashino and character designer Shigenori Soejima revealed on the Persona Stalker Club V talk show that Confidant Hifumi Togo was planned to be an additional party member but was cut due to the story being too long at that point and not wanting to make it longer.

In the Korean and Chinese versions, Ryuji Sakamoto's civilian shoes had their "Rising Sun Flag" symbol removed.

The protagonist's home in the game is Cafe LeBlanc which is a reference to Maurice Leblanc, author of the Arsene Lupin books which the protagonist's initial persona is based and named after.

In the subway station in Shibuya you can find ad posters that scroll to different ads. Here you can find ads for Rise Kujikawa from Persona 4 and Kanami Mashita from Persona 4 Dancing All Night. If you take a confidant to this location you will receive a Rise Poster that you can hang in your room.

When entering momentos for the first time, morgana reveals his ability to turn into a bus stating "For some reason "cats turning into buses" is an extremely widespread cognition among the general public." This is a reference to the Studio Ghibili film My Neighbor Totoro where the Main characters wait for a bus that turns out to be a cat.

In order to Promote the game's release, The Los Cabos restaurant in Shibuya was officially fashioned in the theme of Persona 5 for a limited time.

The designs of the 22 Arcana are based on the Tarot de Marseille, a popular and influential Tarot deck from 16th century France.

During a scene in which the group is talking in Futaba's room, Yusuke will rearrange the poses of Futaba's sentai action figures into the poses of the Ginyu Force from Dragon Ball Z.