In a statement, Nienstedt said he was resigning "to give the Archdiocese a new beginning amidst the many challenges we face."
Auxiliary Bishop Lee Piche also resigned.
The resignations follow the filing of criminal abuse charges against the archdiocese on June 5 and the decision less than a week ago by Pope Francis to approve a new church tribunal
to judge bishops who had failed to protect children
The new court will be part of the powerful Congregation for the Doctrine of the Faith, the Catholic Church's chief watchdog. Since 2001, the congregation has judged priests accused of sexual abuse, but there had been no Vatican office with a similar role to judge bishops.
Also on Monday, the Vatican announced
that its former ambassador to the Dominican Republic, Jozef Wesolowski, will be tried in a church court next month. Wesolowski, 66, is the highest-ranking former Vatican official to be arrested for allegations related to the sexual abuse of minors and the first to be tried on such charges at the Vatican.
The shakeup in the Minnesota archdiocese comes less than two weeks after Ramsey County Attorney John Choi filed six criminal charges
against the St. Paul and Minneapolis Archdiocese, accusing it of encouraging, causing or contributing to the sexual abuse of three victims by a priest in 2010 and 2011.
The priest, Curtis Wehmeyer, was convicted in February 2013 on 20 felony charges of sexual abuse against minors and possession of child pornography, according to the archdiocese.
Nienstedt, who had promoted Wehmeyer, said he leaves "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 had faced allegations of his own, including a 2013 claim
that he inappropriately touched a boy during a public photo session four years earlier. No charges were filed
in that alleged incident.
In July 2014, additional accusations
surfaced of "alleged misbehavior" that "did not involve anything criminal or with minors," according to the archdiocese. At the time, Nienstedt called the allegations "absolutely and entirely false."
Barbara Dorris, outreach director for the victims' advocacy group Survivors Network for those Abused by Priests, welcomed Nienstedt's resignation but called for more.
"Though he has resigned, we still believe Nienstedt should be punished for enabling a predator to hurt kids," Dorris said in a statement. "We hope these Vatican panels will quickly take up the Nienstedt case so that cover-ups will be deterred and kids will be safer."
Pope Francis appointed the Most Rev. Bernard A. Hebda, another archdiocesan official, to serve as interim leader of the archdiocese until a permanent replacement for Nienstedt is named.
Bishop Andrew Cozzens told reporters at a news conference Monday that the archdiocese will "continue to do everything we can to create safe environments for all children," according to CNN affiliate WCCO
"This has been a painful process, a change in leadership offers us an opportunity for greater healing and the ability to move forward," he said.