A barefoot man mumbling to himself set fire to two pews in an Upper East Side church Saturday — and then trashed a popular cafe separated from the church by a glass door.

The crazed man showed up around 12:45 p.m. at the Episcopal Church of Heavenly Rest on Fifth Avenue at 90th Street. Despite his disheveled appearance and muttering in what seemed like an Eastern European accent, no one thought much about him being in the church.

“It’s an open church, and often people start sitting in there,” said volunteer organist Sam Bartlett. “That’s why I didn’t think anything of it when I saw the guy.”

But soon two of the pews in the middle of the large church were set aflame. Bartlett said the flames shot five or six feet into the air.

“All of a sudden everyone came running out,” said Sage Stossel, an artist who was working on a drawing of the church’s exterior.

“People were pointing inside the church. I looked inside the door and saw enormous orange flames in the center.”

Shortly after lighting the pews, the crazy man turned his attention towards the Bluestone Lane Café, which adjoins the church and is separated from its interior by a glass door. He began smashing the door with what witnesses said was a paperweight.

“He was very manic and very angry,” said a café staff worker who declined to give her name.

“He made eye contact and talked to one of the employees, but we couldn’t hear what he said because of the glass.”

Thirty-five cafe’s patrons fled. The café’s 20 staff members grabbed the customers’ belongings as they fled.

“It was very strange, very unusual. Very unsettling for everyone,” said the Bluestone Lane Café’s manager, who also wished to remain anonymous.

The Right Rev. Andrew Dietsche, the Episcopal bishop of New York, went to the church after the fire. “I came here as soon as I got word of what happened,” Dietsche said.

The fire was out by 2 p.m. The disturbed man was taken to New York Presbyterian Hospital for evaluation. No one was reported hurt.

“It’s way too early to talk about motive,” Dietsche said.