Justin Bieber is shrinking his circle and some people who have been cut out say he’s being isolated from longtime friends because he’s in a cult and his church pastor is wielding a ton of influence over his life … but the pastor says that’s bogus.

TMZ has a new documentary, “TMZ Investigates: What Happened to Justin Bieber,” now available on Hulu, and part of our investigation digs into Justin’s involvement in his church, Churchome, in Beverly Hills.

Justin is no longer friends with Ryan Good, the best man at Bieber’s wedding and the creative director at JB’s fashion brand Drew House, and our sources say it has to do with Ryan leaving Churchome because he thought it was a cult.

We were told Justin and Judah confronted Scooter Braun, who is Jewish, about not believing in Jesus … and that they also were badgering Ryan about his sex life.

Some comments from Justin’s business manager and fellow Churchome member also raised red flags for some … we get into it all in the documentary while also exploring Justin’s mental health, marriage, money troubles and career.