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 on January 4.

Story developing ...