The “spiritual leader” of a Queens offshoot Catholic church has been arrested for sexually abusing a 12-year-old boy, authorities said Friday.

Jese “Jesse” Milagrosa, the 69-year-old “bishop” of Our Lady of La Salette Church in Bayside, was arraigned before a Queens judge on charges of predatory sexual assault against a child, first-degree course of sexual conduct against a child and first-, second- and third-degree criminal sexual act, according to borough DA John Ryan.

Police nabbed Milagrosa with the help of the boy, said the criminal complaint against the defendant. Last year, the victim confronted his alleged attacker about the abuse — and recorded the exchange.

“That was my mistake,” Milagrosa is allegedly heard saying on the recording. “If you want to report this and I’ll pay the consequences … I know I’m going to prison, I know it will be for a long time.”

Ryan said in a statement, “The defendant is accused of using his position as head of the church to take advantage of an innocent child for his own sexual gratification.”

Milagrosa pleaded not guilty to the charges.

“We deny these accusations and urge everyone to avoid rushing to judgment and instead await the outcome of the judicial process,” said Jeffrey Pittell, Milagrosa’s lawyer.

If convicted, Milgrosa faces between 10 years to life in prison.

The church is not affiliated with the Diocese of Brooklyn, which includes Queens.