Dan Bongino has said he will leave his role as the FBI’s deputy director in January.

In a post on X, he thanked President Donald Trump, as well as the director of the FBI and the attorney general “for the opportunity to serve with purpose”.

It comes after Trump said earlier on Wednesday that the former podcast host “did a great job” in office, and “wants to go back to his show”.

Bongino, who was appointed to the role by Trump in February, was previously a New York City police officer and a US Secret Service agent assigned to protect Barack Obama. In recent years, he built a large following through his podcast and other media appearances.

Bongino, a staunch Trump ally, was considered a surprise pick for the role – which had previously been held by career agents – because he had no prior experience with the agency.

The FBI Agents Association, which represents around 14,000 current and former agents, had opposed his appointment to the position.

Announcing his decision in a social media post on Wednesday, he said: “I will be leaving my position with the FBI in January. I want to thank President Trump, AG [Pam] Bondi, and Director [Kash] Patel for the opportunity to serve with purpose.

“Most importantly, I want to thank you, my fellow Americans, for the privilege to serve you. God bless America, and all those who defend Her.”

Before joining the agency, Bongino had echoed disinformation and conspiracy theories about Trump’s false claim that he won the 2020 election, and about the 6 January 2021 pipe bomb investigation.

Bongino had previously called the pipe bomb case an “inside job”. After taking office he pushed to make the investigation, which Attorney General Bondi said had “languished”, a priority for the FBI.

Earlier this month, a man with no known ties to the government was arrested, nearly six years after the pipe bombs were discovered outside the national headquarters for the Republican and Democratic parties.

FBI Director Patel, in a social media post on Wednesday praising Bongino’s tenure, said he had “served as the people’s voice for transparency, and delivered major breakthroughs in long unsolved cases like the pipe bomb investigation”.

“He not only completed his mission – he far exceeded it,” Patel wrote.

Bongino also appeared to change his mind about the death of sex offender Jeffrey Epstein once he became a leader at the FBI.

As a commentator, he had questioned whether Epstein took his own life in a New York prison cell in 2019 while awaiting trial. Then, in May, Bongino said: “I have seen the whole file. He killed himself”.

In July, the US justice department and FBI released a memo that said Epstein did take his own life, and did not have a “client list”.

The memo frustrated many of Trump’s supporters, who echoed the Epstein conspiracy theories and rejected the justice department’s findings.

According to the BBC’s media partner CBS News, the memo led to a contentious meeting between him and Bondi.

Bondi, who oversees the FBI, wrote in a brief post on X on Wednesday that “Americans are safer” because of Bongino’s FBI service.