“I have accepted Father Conroy’s letter and decided that he will remain in his position as Chaplain of the House,” Ryan said in a statement. “It is my job as speaker to do what is best for this body, and I know that this body is not well served by a protracted fight over such an important post.”

Ryan said he plans to meet with Conroy next week “so that we can move forward for the good of the whole House.”

In a fiery letter to the speaker announcing plans to stay in the job through at least the end of this year, Conroy challenged Ryan’s authority to fire him from the post — a position elected by members of the House — and questioned the reasons Ryan had given for his dismissal.

Conroy also hinted that his ouster was due to an anti-Catholic bias based on a conversation he had with Ryan’s chief of staff when he was asked to retire. Ryan did not address that conversation, but his chief of staff issued a statement expressing disagreement with Conroy’s recollection.

“My original decision was made in what I believed to be the best interest of this institution,” Ryan said. “To be clear, that decision was based on my duty to ensure that the House has the kind of pastoral services that it deserves.”

House Minority Leader Nancy Pelosi (D-Calif.) cheered Ryan’s decision but cautioned this isn’t the end of the story.

“Speaker Ryan’s decision to accept Father Conroy’s decision to rescind his resignation and finish his term is welcome news,” Pelosi said in a statement Thursday night. “However, many distressing questions must still be answered about the motivations behind Father Conroy’s unwarranted and unjust dismissal.”

Ryan has said publicly and privately that forcing Conroy to resign also had nothing to do with politics, and that he came to the decision after several members complained that their “pastoral needs” were not being met by the priest.

But Democrats and some Republicans have questioned Ryan’s explanation, speculating the decision had more to do with internal pressure from Republican evangelicals than anything Conroy may have done.

Conroy also challenged Ryan’s assertions in his two-page missive to the speaker.

“I have never been disciplined, nor reprimanded, nor have I ever heard a complaint about my ministry during my time as House Chaplain,” Conroy wrote. “You may wish to outright ‘fire’ me, if you have the authority to do so, but should you wish to terminate my services, it will be without my offer of resignation, as you requested.”

Conroy submitted his resignation in mid-April, at the request of Ryan, with an effective date of May 24. But the controversy surrounding his departure didn’t erupt until last week, when lawmakers learned Conroy’s decision was not voluntary.

In the letter, Conroy speculated Ryan’s decision was much more political than the speaker has let on. Ryan did not personally reach out to Conroy to request his retirement, instead sending his chief of staff, Jonathan Burks, to deliver the news in an April 13 conversation.

But Burks never mentioned problems with the way Conroy conducted his ministry or outreach to members during that conversation, he wrote in the letter. Instead, Burks said the move had to do with an interview Conroy gave to National Journal in January, a prayer he delivered on the GOP tax bill in November and his Catholicism.

“I inquired as to whether or not it was ‘for cause,’ and Mr. Burks mentioned dismissively something like ‘maybe it’s time that we had a Chaplain that wasn’t a Catholic,’” Conroy wrote.

Burks rejected that characterization Thursday evening.

“I strongly disagree with Father Conroy’s recollection of our conversation,” he said in a statement. “I am disappointed by the misunderstanding, but wish him the best as he continues to serve the House.”

AshLee Strong, the speaker’s spokeswoman previously dismissed the notion that Ryan, a Catholic, would want to fire the chaplain based on his religious beliefs.

“The speaker is a proud, deeply Catholic person and this charge is not only false but outrageous,” Strong said in a statement last week.

Conroy did not return a request for comment Thursday. In the letter, Conroy said he only submitted his resignation because he thought Ryan had “the absolute prerogative and authority” to force his ouster.

But, after seeking the “advice of counsel,” Conroy said he no longer believed that to be the case and plans to stay in the job through the end of this Congress — and possibly longer if re-elected by the members.

“Had I known of any failure in providing ministry to the House, I would have attempted to make the appropriate adjustments, but in no case would I have agreed to submit a letter of resignation without being given that opportunity,” Conroy wrote.

Conroy was first appointed to the post in 2011 by then-Speaker John Boehner (R-Ohio). He is the first Jesuit priest and only the second Catholic to hold the position, which has been in place since 1789.

In his role, Conroy is responsible for delivering the opening prayer during each House session and provides ministerial counseling to members who request his services.

The questions surrounding Conroy’s abrupt retirement ignited a political firestorm in the House, with Democrats seizing on the issue as Ryan unsuccessfully tried to calm brewing dissent within his own conference.

Democrats demanded an investigation into the chaplain’s forced resignation, going so far as to force a floor vote on the issue last week. The vote failed but not before a handful of angry Republicans defected from the party line in a show of solidarity with the chaplain.

Ryan tried to quell the controversy during a private GOP conference meeting last Friday morning, telling lawmakers his decision only came after several members complained that their “pastoral needs” weren’t being met.

Ryan repeated his explanation during a public appearance in Milwaukee on Monday: “This was not about politics or prayers, it was about pastoral services. And a number of our members felt like the pastoral services were not being adequately served, or offered.”

Conroy openly challenged the speaker’s reasoning on Thursday.

“This is not the reason that Mr. Burks gave me when asking for my ‘resignation,’” he wrote. “In fact, no such criticism has ever been leveled against me during my tenure as House Chaplain.”

Democrats and some Republicans have also dismissed Ryan’s reasons, saying they believed the speaker was facing pressure from evangelicals within the GOP conference to find a chaplain whose politics more closely aligned with theirs.

During the GOP conference meeting last week, Rep. Peter King (R-N.Y.) confronted Rep. Mark Walker (R-N.C.), a Baptist pastor, for comments Walker made to reporters about the next House chaplain needing to have a family.

Walker’s remarks were interpreted by some as being biased against Catholics given that priests take a vow of celibacy. Walker apologized for the comments, saying he misspoke, but King later told reporters he still felt political pressure may have played a role in the chaplain’s ouster.

“To be the first House chaplain to be removed in the history of Congress, in the middle of a term, raises serious questions,” King said at the time. “I think we deserve more of an explanation of why. Was there political pressure?”