Persona 1-5 all take place in the same universe and timeline

However, the nature of that timeline has changed between Persona 2 and Persona 3 due to an internal cosmic ‘retcon’ that altered the nature of reality. 

Persona 3 directly references the main characters of Persona 2, and it is therefore possible to say that they canonically exist in the same universe.

👉 Persona 3 also directly references the Nanjo group from Persona 1, saying that the Kirijo group split off from it. It is implied, but not stated outright that this was over a disagreement about shadow/persona research resulting from appropriating SEBEC’s DEVA system.

👉 According directly to Persona 3, the characters and entities of Persona 1 and 2 absolutely canonically exist in its timeline.

👉 Therefore, since characters from Persona 4 and 5 both directly interact with characters from Persona 3, it is absolutely and unquestionably canonical that all of these games exist within the same universe.

👉 So what happened between Persona 2 and 3 to change the nature of the persona universe? How does it fit together, and why does it change?

• Prior to the end of Persona 2: Eternal Punishment in 2000, Philemon and Nyarlathotep have a wager about the nature of humanity and whether it will destroy itself.
• Nyarlahotep gives humanity the power of rumor in an attempt to metaphorically ‘give them the rope to hang themselves with’, manipulating people with rumors to change reality and lead itself to destruction.
• At the end of Eternal Punishment the characters “manage to defeat and banish him from the Persona universe, allowing Philemon to win the bet and eradicate the power of rumors once and for all.” (wording directly from the Persona wiki)

that means–

• Reality takes a concrete shape and can no longer be influenced by rumor and belief.
• Due to reality’s newly concrete nature, the powers of rumor and belief gather in pockets of subreality such as Mementos, The Dark Hour and the TV world where they reflect human desire.
• The Velvet Room closes its doors to the public.
• Philemon disappears disappears into the background
• Nyarlahotep disappears into the background
• a number of new forces representing Nyarlahotep’s views appear to threaten humanity
• Due to the power of rumor disappearing, Personas can no longer be summoned by ritual, and are instead unlocked by users due to trauma and circumstance.

We can infer that–

• due to being banished from the universe and unable to intervene directly, either Nyalahotep began to act through proxies (such as Nyx) or the power vacuum resulting from Nyalahoteps absence in the universe retroactively created these independent avatars of humanity’s desire for destruction.
• due to the power of rumor no longer being active, people can no longer use the rumored summoning ritual to gain a Persona, and Personas must therefore be unlocked in different ways.
• Because the world of the collective unconscious (dark hour, tv world, mementos) is kept away from the world at large there is no longer a reason for the Velvet Room to be a public ‘club’. It closes its doors to all but special demand.

The Persona games, 1-5 and relevant spin-offs, all take place in the same single universe, in a timeline in which the nature of the universe was changed at the end of Persona 2 and continuing forward from there with a different structure.

In a way you can liken the end of Persona 2 to the same biblical punishment that it references– being cast out of “eden ” a place where dreams come true, and forced into the cold, hard permanence of the ‘real’ world. 

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Here’s a look at exactly what changed between the Malleable Persona Reality (pre-2000) and the Permeable Persona Reality (Post-2000)

The world of Persona 1 and 2 (the Malleable Persona reality):

The Velvet Room: Appears as a nightclub and can be accessed by anyone with a persona, or potentially even anyone with a link to the collective unconscious. 

Igor: A servant of Philemon who takes care of persona fusion for anyone who enters the Velvet Room.

Personas: Thanks to the power of rumor a persona can be summoned by anyone who enacts the correct summoning ritual.
Philemon: A benevolent observer and guardian of humanity. He has a wager with Nyarlathotep that humanity will overcome their baser nature and reject their own destruction. 

Nyarlathotep: A malefactor of humanity who believes that humanity truly wishes to destroy itself and cannot overcome this urge for destruction. To this end he directly intervenes in human affairs in a bid to tempt humans to destroy themselves.

The nature of reality: Malleable. Reality can directly be changed by the beliefs or worldview of the collective unconscious.

The world of Persona 3-5 (The Permeable Persona reality):

The Velvet Room: Can only be accessed by those who have made a contract with Igor. This space is used by the protagonist to unlock the deeper power of Personas that those without contracts don’t have access to.
Igor: A spiritual guide who makes contracts with people who have a certain destiny.

Personas: Personas are summoned by people who have experienced a severe trauma of some kind, whether an experience of death, a separation from their shadow self or true nature.
Philemon: Only seen or referenced in the form of a blue butterfly.

Nyarlathotep: Absent. Replaced by other avatars of humanity’s desire for destruction such as Nyx.

The nature of reality: Concrete, but permeable. Reality can no longer be directly changed by the beliefs or worldview of the collective unconscious. Instead, these beliefs create separate layers or pockets of their own reality (Tartarus, the TV world, Mementos etc) which can be entered by certain persons and when growing too strong can threaten to intrude on the concrete reality above.

Abbreviated timeline:

• 1996: SEBEC DEVA system experiments
• 1996: Events of Persona 1
• August 1999: Events of Persona 2 Innocent Sin
• 1999: Kirijo group experimenting with SEBEC tech– after the change in the universe this becomes Shadow research.
• February 2000: Events of Persona 2 Eternal Punishment retroactively affecting the P3 timeline
• Summer 2000: Aigis catches Death and imprisons him in P3MC
• 2009: Persona 3 starts
• 2011: Persona 4 starts
• 2016: Persona 5 starts