The district attorney's chief of special investigations, Patrick Blessington, told Common Pleas Judge M. Teresa Sarmina that in the spring of 1999, Avery, while serving as a priest at St. Jerome Parish in the Northeast, "engaged in oral sexual intercourse" with a then-10-year-old altar boy.
The judge on Wednesday had given Avery's defense team a win when she ruled that the jury could hear about the now-young man's troubled past - his expulsion from the Catholic high school he attended in the early 2000s, and of discrepancies in the man's related civil lawsuit and his grand-jury testimony.
It is unclear why Avery decided to enter his plea. Attorneys in the case are under a gag order.
Monday's trial will continue with defendants Monsignor William Lynn, 61, the first U.S. Catholic Church official charged with concealing priest sexual abuse, and the Rev. James Brennan, 48, charged with raping a boy.
At Thursday's hearing, Blessington also told the judge that Avery conspired to endanger the welfare of children along with Lynn and/or other Archdiocese of Philadelphia officials and employees from 1992 through 2003.
He cited the example of a person who in 1992 "reported to Lynn that Avery had sexually abused him when he was a minor after he had assisted Avery with a disc-jockey job in West Philadelphia."
Avery was then a priest while Lynn served as the secretary for clergy.
Blessington said Avery and archdiocesan officials acted in concert to conceal Avery's "known acts of sexual abuse" of this minor "so that Avery could remain in ministry without the knowledge of parishioners . . . "
Avery was "not supervised when he interacted with altar servers or other parish children at St. Jerome's" and "continued to perform as a disc jockey with the knowledge of Lynn and others in the Archdiocese for several years," Blessington said.
Avery, represented by attorney John P. Donohue, acknowledged to the judge that he willingly entered his guilty plea, but later declined his right to speak in court.