ST. PAUL — Archbishop John Nienstedt’s leadership of the Archdiocese of St. Paul and Minneapolis unraveled over a painful two years.

A church archivist accused him of leaving abusive clergy in parishes and church jobs without warning parents or police. A task force he appointed confirmed the archdiocese had been negligent. Around the same time, he faced allegations of his own inappropriate sexual conduct, but he didn’t reveal specifics.

Through it all, Nienstedt rejected calls for his resignation. Then, less than two weeks ago, a prosecutor brought child-endangerment charges against the archdiocese, and on Monday, he stepped down.

“I leave with a clear conscience knowing that my team and I have put in place solid protocols to ensure the protection of minors and vulnerable adults,” Nienstedt wrote in the announcement.

But the Rev. Michael Tegeder, a Minneapolis priest and frequent Nienstedt critic, said the archbishop “came into this diocese without really any empathy” and “undermined so many of the good things that were going on here.”

“He had to go,” Tegeder said.

Nienstedt’s resignation was announced by the Vatican, which also said it had indicted Jozef Wesolowski, its former ambassador to the Dominican Republic, on charges of sexually abusing minors in the Caribbean country and possessing child pornography. He will be the highest-ranking Vatican official ever to stand trial for a sex crime.

When the Minnesota crisis erupted, Nienstedt had his defenders, but he couldn’t bank on widespread support in the archdiocese. Appointed in 2008 by Pope Benedict XVI, Nienstedt took a much harder line than his predecessor, Archbishop Harry Flynn, on upholding Catholic orthodoxy. As bishop of nearby New Ulm, Nienstedt had chided a priest who worshipped with Lutherans after a tornado destroyed his Catholic church, and, in his diocesan newspaper, Nienstedt warned parishioners not to attend the movie “Brokeback Mountain” because it showed sex between two men.

As Minneapolis archbishop in 2010, he made a high-profile drive for a constitutional amendment that would define marriage as the union of a man and a woman by appearing in a DVD that was mailed to several hundred thousand Minnesota Catholic families. Many local Catholics and clergy felt alienated by his style and emphasis.

“He was out of step with the archdiocese. He did not respect the people, did not respect his priests, did not engage in dialogue,” said Charles Reid, a professor in canon law at the University of St. Thomas. “He was an autocrat.”

Then in May 2013, Minnesota lawmakers lifted time limits for lawsuits brought by child sex-abuse victims. As attorneys started filing lawsuits, the archdiocese took a hit from within: The archivist, canon lawyer Jennifer Haselberger, who had worked for the archdiocese for five years, went public with accusations that church leaders covered up for an abuser and kept him on assignment.

She made a stream of allegations over the next year, accusing bishops and top archdiocesan staff of lying to the public and the U.S. Conference of Catholic Bishops, using a chaotic record-keeping system that helped conceal the backgrounds of guilty priests still in ministry and failing to monitor abusive clergy as promised.

Haselberger’s allegations hit especially hard because they came nearly a dozen years after U.S. bishops, at the height of the national clergy sex-abuse crisis, pledged to remove all guilty clergy from church work.

The archdiocese insisted child safety was its highest priority, and Nienstedt pledged to prove it. He appointed the task force that looked into the archdiocese’s record on abuse cases and promised to implement the committee’s recommendations. But he was working in the shadow of allegations of his own misconduct. A boy accused him of inappropriate touching in a public setting, which police concluded was unlikely.

Then Nienstedt revealed he had hired a law firm to conduct another investigation into his conduct, this time over allegations of inappropriate sexual behavior with seminarians and priests. The archdiocese has not released the findings.

Nienstedt said he was innocent and would press on as archbishop despite demands he step down.