Aubrey Plaza and her late husband Jeff Baena were separated for several months before he took his own life … TMZ has learned.

Aubrey and Jeff’s marital difficulties are revealed in the Medical Examiner’s report … in the documents, obtained by TMZ, the ME notes Jeff was separated from his wife since September 2024.

The ME says Jeff’s manner of death is suicide … which lines up with what we were originally told by our law enforcement sources.

TMZ broke the story … Aubrey’s husband was found dead in his Los Angeles-area home back in January.

The ME’s death investigation summary says Jeff’s dog walker found him dead in his home and called police.

Officers say the dog walker told them she showed up to his home on January 3 at her normal time to walk his dog, and she heard loud music coming from within the house, which was unusual. She says she unlocked the front door to find his body.

Cops say they were told Jeff had been separated from Aubrey since September 2024 when she moved to New York … and officers note they were told Jeff had a phone conversation with Aubrey the night before he was found dead.

Police say they spoke to Aubrey on the phone after he was found dead and she confirmed their separation. Officers also say Aubrey told them Jeff made concerning remarks in October 2024 which prompted her to call a friend to perform a welfare check on her husband.

Cops say Aubrey told them Jeff had been attending therapy since the alleged October incident and she claimed he did not have any previous suicide attempts.

The ME says Jeff was pronounced dead at 10:39 AM PT on January 3 and police say Aubrey told officers she last heard from him earlier that morning at 7:36 AM PT when he sent her a text message.

The docs say no illicit drugs or alcohol were found on the scene or in Jeff’s system and no suicide note was found.

Aubrey and Jeff married in 2021 … and Aubrey described the lowkey affair on an episode of “The Drew Barrymore Show.”