WASHINGTON >> A day before Geoffrey S. Berman was axed from his job as head of the U.S. Attorney’s office in Manhattan, he refused to sign onto a letter crafted by senior officials in Washington lambasting New York’s mayor for putting COVID-19 restrictions on religious gatherings.

Berman’s refusal didn’t directly contribute to his ouster. But it was another example of the ways in which he appeared to run afoul of Attorney General William Barr and other high-ranking officials at the Justice Department.

According to several people familiar with their relationship, Berman, a political donor to President Donald Trump who investigated and charged some of his allies, wasn’t a team player. He operated outside Washington leadership, and won praise from Trump critics as an independent thinker. And he had refused to even alert Washington to cases his high-profile department was working on. The people were not authorized to speak publicly and spoke to the Associated Press on condition of anonymity.

As a result, Berman’s job often appeared to be in jeopardy. He was never formally nominated to the post by Trump, despite having been personally interviewed for the job by the president. Instead, he was installed by a federal court.

As this year wore on in the wake of the prosecution of Rudy Giuliani’s associates and the probe of the former mayor, his allies in the prosecutor’s office were surprised each time Berman returned from Washington with his job intact.

“The most surprising thing is that he’s held on as long as he has,” said Danya Perry, a former Manhattan federal prosecutor who represented California lawyer Michael Avenatti in his recent fraud trial defense.

The tensions between Berman and the Justice Department reached a breaking point Friday, when Barr issued a surprise press release saying Berman had resigned and would be replaced by the Securities and Exchange Commission Chairman Jay Clayton, a lawyer who has virtually no experience as a federal prosecutor. Berman refused to step down, and went into work Saturday. He eventually consented to leave after Barr said Trump had officially fired him and the second in command of the office would take over.

One of Berman’s final acts was to refuse to sign onto a letter criticizing New York Mayor Bill de Blasio for allowing massive police reform protests even though he had cracked down in April on a group of thousands of mourners at a funeral for a Hasidic leader whose death was reportedly linked to the coronavirus, the people said.

The Hasidim are an insular, ultra-orthodox Jewish sect in Brooklyn. It is a powerful voting bloc that favored Trump in 2016.

“The message to the public from New York City’s government appears to favor certain secular gatherings and disfavor religious gatherings,” wrote Assistant Attorney General Eric Dreiband.

Ensuring religious liberty has been a top priority for Barr, whose office has weighed in on several lawsuits around the country seeking to reopen religious gatherings during the pandemic.

The Justice Department sent separate letters last month to the governors of Nevada and California warning that religious gatherings should be held to the same standard as similar secular gatherings when it comes pandemic-related public health orders. The letter sent to California Gov. Gavin Newsom was signed by all four U.S. attorneys in the state.

The final straw for Berman, though, remains murky. Justice Department officials insisted the de Blasio letter played no role and Barr didn’t know about Berman’s refusal to sign it when he sent out the statement. They said Berman was offered other positions, including running the Justice Department’s Civil Division, but declined them. New Yorkers close to Berman were mystified, especially because the probe into Giuliani is ongoing, and no indictments were imminent.

White House spokeswoman Kayleigh McEnany said Trump holds Clayton in high regard and wanted to nominate him to the job so he could stay in government, since he planned to move to New York.

“Barr was working on a smooth transition, and when Berman chose to respond in the way that he did, he came to the president, and the president agreed and fired this individual, Mr. Berman, as Mr. Clayton now will, in time, get to that position,” she said.

Berman initially vowed to stay on the job until a replacement was confirmed. He changed his mind late Saturday after he was formally fired, and Barr said he would allow the second in command, Deputy U.S. Attorney Audrey Strauss, to become acting U.S. attorney.

Among the most high-profile investigations he was overseeing was into Giuliani’s business dealings, including whether he failed to register as a foreign agent.

The Southern District has also prosecuted a number of Trump associates, including Trump’s former personal lawyer and fixer Michael Cohen, who served a prison sentence for lying to Congress and campaign finance crimes.

Berman has overseen the prosecution of two Florida businessmen, Lev Parnas and Igor Fruman, who were associates of Giuliani and tied to the Ukraine impeachment investigation. The men were charged in October with federal campaign finance violations, including hiding the origin of a $325,000 donation to a group supporting Trump’s reelection.

And only days ago, allegations surfaced from former Trump national security adviser John Bolton that the president sought to interfere in an investigation by Berman’s office into the state-owned Turkish bank in an effort to cut deals with Turkish President Recep Tayyip Erdoğan.