Henning takes over from Cardinal Sean O’Malley, who is retiring after serving as archbishop of the nation’s fourth-largest archdiocese for 21 challenging years. Much of his tenure was dominated by the fallout from the clergy sex abuse crisis.

As the procession began, Henning knocked three times on the cathedral doors and was greeted by O’Malley, who embraced Henning with a hug.

Among the guests were Cardinal Christophe Pierre, Apostolic Nuncio to the United States, five additional cardinals, five archbishops, more than 50 bishops and nearly 500 priests, religious, deacons, seminarians and lay people.

Before Henning officially became archbishop, Pierre read an English translation of the papal bull, or decree, from Pope Francis appointing him to the position. Henning then showed the bull to the Archdiocese’s College of Consultors, which they inspected to ensure that the papal seal was genuine. Once accepted, Henning presented the bull to the entire congregation.

At that point, Henning, 60, was ushered to the archbishop’s “cathedra,” or seat, and formally assumed the role as the congregation stood in applause.

During his first remarks as Archbishop of Boston, Henning drew laughter from the congregation as he first joked that the most common question he gets is whether he is or will become a Red Sox fan (he did not specifically answer.)

He then spoke about his faith, which led to a reflection on the church’s years of failure to protect children who have been sexually abused. He praised the courage of survivors who came forward with their stories.

“This church in Boston, it is in a very real sense a church wounded by a failure to act with compassion and healing,” Henning said. “Sins against the innocent. We have seen over these decades a passionate effort to protect the vulnerable, yet we still feel the weight of those wounds.

“And we owe a debt of gratitude to the victims, the survivors, who are telling their stories, because they have helped protect new generations through their courage and their prophetic truth telling,” he continued. “And in living the faith, in their capacity for compassion and solidarity of love towards their neighbor, they become, for us, hope in the midst of the world, a light in the darkness.”

Henning inherits an archdiocese that is in much better shape than the one O’Malley faced in 2003. At the time, the archdiocese had been severely crippled, financially and spiritually, by the clergy sex abuse crisis. Its finances were under water, parishioners were outraged by impending church closings, and both mass attendance and Catholic school enrollment were declining.

Now the archdiocese is in the black: parishes have consolidated and regrouped, school enrollment appears to have stabilized, and 11 priests have been ordained this year, the second highest number since 1997.

Also in attendance were Henning’s parents, Richard and Maureen, as well as Boston Mayor Michelle Wu and other faith, government, business and parish leaders in the archdiocese. Henning thanked Wu and the Boston Police Department for their help in the day’s events.

Near the end of the Mass, Henning thanked his family and friends who “have shaped and guided me throughout my life.” He recognized his parents, who were seated in the front row, and the congregation rose and applauded.

“Thank you for that,” he told the audience. “They deserve it, they are the best of people.”

He also recognized O’Malley and his leadership years in Boston.

“The quality of your service has always been a truly humble gift from you for the sake of others,” Henning said. “He was compassionate, he was gentle, and he was truly biblical and authentic to the faith. . . . You, in a very real sense, are a foundation upon which we will continue to build.”

In his two decades as archbishop, O’Malley has been credited with opening and maintaining a dialogue with abuse victims, who have received more than $175 million in settlements since 2002, according to the archdiocese.

But the cardinal has also faced criticism for his handling of the fallout from the priest sex abuse scandal, particularly in 2011 when he released the names of archdiocesan clerics who had been accused of abuse. Although 159 clerics were named, the list omitted the names of 91 others.

As the procession gathered outside the cathedral on Thursday, a group of people with the Survivors Network of Abused by Priests (SNAP) held a protest nearby.

Claude LeBeouf, 71, held a sign that read “Child sexual abuse is a spiritual crime.” LeBeouf said it was sexually abused by the late Reverend James Porterwho was convicted of molesting over two dozen children. He said he believed Henning helped cover up sexual abuse by priests.

“He may not be an abuser, but he was complicit in covering up the abuse,” LeBeouf said.

Another demonstrator, Dr. Robert Hoatson, a former priest and sex abuse survivor who co-founded the group Road to Recovery, said the Boston Archdiocese needs to create an easier process for abuse victims to obtain compensation. He pointed to recent news the Archdiocese of Los Angeles has agreed to pay $880 million to victims as an example Boston should follow, but expressed skepticism that Henning would be the change agent he was hoping for.

“Here comes another archbishop who is of the same ilk as Sean O’Malley and all the others who came before him,” Hoatson said.

In a pre-recorded interview broadcast during a live stream of the procession, Henning said he was committed to ensuring children are protected from abuse.

“I hope it’s encouraging when I say that it’s a central commitment that I’ve made in my life over many years,” he said. “We work hard to ensure that the children in our care are safe, fed and treated with God-given dignity. I certainly feel, along with the whole church, a sense of pain that there were young people who did not have this kind of protection and who suffered because of it.”

Henning, who most recently served as bishop of Providence, was auxiliary bishop for the Rockville Center Diocese of Long Island, NY when his bishop filed for bankruptcy four years ago. The case has sparked an ongoing legal battle with 650 survivors of settlement abuse.

The case was sent to mediation in May after most survivors rejected a proposed $200 million settlement and the archdiocese sought to dismiss bankruptcy.

Henning defended the decision to file for bankruptcy.

“It was really the only decision that would have allowed the diocese to fulfill its obligations to the survivors as well as continue the mission of the church,” he said, adding that he had only a limited role in the proceedings.

Henning was asked at his introductory press conference in August how he would reach out to Catholics who left the church because of the abuse scandal. “I will listen to their pain and their wounds,” he said.

Boston attorney Mitchell Garabedian, who has represented hundreds of child sexual abuse survivors, including those molested by priests in Boston, said many victims “feel as though the removal of Cardinal O’Malley and the installation of Archbishop Henning will create a new layer of irresponsibility. .”

“Archbishop Henning may say all the right things about clergy sexual abuse, but he will not implement any meaningful programs to protect children from being sexually abused or to help victims try to heal,” Garabedian said in a statement . “In other words, Archbishop Henning will further distance the Archdiocese from the clergy sexual abuse crisis and make the crisis a forgotten thing of the past.”

Nick Stoico can be reached at [email protected]. Brian MacQuarrie can be reached at [email protected]. Izzy Bryars can be reached at [email protected]. Follow a @izzybryars.