Worshippers at a Bronx Catholic church broke into applause Sunday when a letter from their disgraced priest was read before Masses announcing he was stepping aside in the wake of a humiliating sex scandal.

The Rev. Peter Miqueli was nowhere to be found at St. Frances de Chantal Church when another priest read a letter from him, causing cheers to break out.

Craig Burner, one of the cheering parishioners, said Miqueli should have been out months ago.

“He was just mean and nasty. His letter is a lie,” Burner said. “We reported him to the archdiocese, and they said they would look into this, but they never did.”

Miqueli is being investigated for allegedly lifting church funds to pay for private boy toy Keith Crist, a muscular S&M master.

Parishioner William Doucet said he grew so suspicious of Miqueli that he stopped using cash for the collection plate.

“I stopped giving money in my envelope and would only write a check when I heard about the funny business with the money,” Doucet said.

But Miqueli wasn’t totally without backers, as Thersea Chirinnos yelled out in support of him Sunday: “He will come back!”