A former Bronx charter school orchestra conductor sexually abused four students for years — including at least one girl who was just 12 when the molestation started, prosecutors say.

Jesus Concepcion, 48, was known as “Mr. C” at KIPP Academy Middle School, where the music teacher and orchestra instructor preyed on the girls from 2002 through 2007 by luring them into sex acts in his car, at motels and in the public charter school’s music room, according to the US Attorney’s Office for the Southern District of New York.

After singling his victims out with “personal attention,” Concepcion plied the students with money, clothing, jewelry and other gifts while telling several of them that they were in a romantic relationship, federal prosecutors allege.

Concepcion was arrested Saturday, four years after accusations against him at the school surfaced and were reported to authorities, officials said.

He is accused of also taking his victims from KIPP Academy or other locations in the Bronx to motels in New Jersey, where he typically told them to stay in his car as he got a room, authorities said.

In at least one instance, he then had sex with a female student in a motel against her will, prosecutors said.

Concepcion is accused of continuing to sexually abuse two of his victims after they went to high school. Prosecutors said he visited them in early 2003 or 2004 while they were freshmen at an out-of-state high school and had sex with them in his car, prosecutors said.

Concepcion, who taught at KIPP Academy from 2000 through 2007, was terminated for “misconduct with a student,” school officials told parents in a statement Monday. Two alumni reported the accusations in 2017, officials said.

KIPP NYC staffers have cooperated with law enforcement since the accusations were reported four years ago, a rep told The Post on Tuesday in a statement.

“We are deeply saddened that former students experienced abuse while attending a KIPP NYC school,” the statement read. “We are hopeful that with today’s arrest justice will finally be served.”

Concepcion, of Simpsonville, SC, was arrested in Charlotte, NC.

He’s facing four counts each of enticing a minor to engage in illegal sexual activity and transporting a minor to engage in illegal sexual activity. He’s also accused of enticing one of his victims to send him naked photographs of herself using a cellphone he gave her, prosecutors said.

He faces up to life in prison if convicted.

“Teachers serve as trusted figures to their students as they work to educate and prepare them for the future,” FBI Acting Assistant Director Jacqueline Maguire said. “As alleged, Mr. Concepcion egregiously breached that trust as he abused his position to coerce students — some as young as 12 years old — into having sex with him.”

Concepcion denies the allegations and plans to plead not guilty, his attorney told The Post.

“He will challenge every charge lodged against him, and will expose the untruth in the statements made by his accusers,” Charlotte-based attorney Rob Heroy said in a statement.

Concepcion was previously described as a “father figure” by some students while teaching at Bronx Preparatory Charter School, where the popular instructor resigned for “personal reasons” in March 2001, the New York Times reported.

Concepcion served as the school’s “informal dean” and was known for his “tough-love blend of hugs, humor and high expectations” from students there, including some who considered him a role model.

Concepcion at the time had returned to KIPP Academy, where he left the previous fall to work at Bronx Prep, the Times reported.

“He was the heart of Bronx Prep,” one sixth-grader wrote in a school newspaper article about Concepcion being named teacher of the month. “How will we live without him?”

Concepcion, meanwhile, said he quit Bronx Prep because he wasn’t fulfilled there.

“If I’m not happy, I’m not productive,” he told the Times.