Miller was being held on $20,000 bail and was scheduled to appear in court Wednesday, Orange County jail records showed.
The pastor at Mission Hills Church in Mission Viejo called authorities when he found evidence of a break-in Monday morning, including books and CDs that were strewn about, white powder on the floors and missing boards from a previously broken window, sheriff's spokesman Jim Amormino said.
Deputies arrived and said they found Miller naked on a couch.
"When they asked him his name he responded, `Mayhem,' " Amormino told the Orange County Register.
They also found evidence that Miller had set off fire extinguishers inside the church, Amormino said. Miller was coherent and cooperated with authorities as he was arrested.
Miller, a popular professional middleweight in the mixed martial arts world, has fought for several organizations including UFC, but has lost three of eight fights.
He also hosted the MTV show "Bully Beatdown," a reality show where bullies are challenged to take on professional MMA fighters for a chance to win money.
Before his last fight on May 27, Miller said he would retire if he was defeated, and went on to lose a lackluster decision to C.B. Dollaway