Questions are swirling inside the FBI after Attorney General Pam Bondi and FBI Director Kash Patel made the unprecedented move of naming Missouri Attorney General Andrew Bailey as co-deputy director of the bureau — a first in the agency’s history.

The announcement comes amid rising tensions with current Deputy Director Dan Bongino, who has been under a microscope since a falling out with Bondi over the handling of the Jeffrey Epstein files last month, CNN reported.

Bailey will now serve alongside Bongino in the number-two role, Patel and Bondi confirmed to Fox News Digital, which first broke the story. Bongino, who was appointed as the FBI’s sole deputy director earlier this year, shocked colleagues in July when he largely isolated himself from internal operations following the Epstein files dispute.

“I am thrilled to welcome Andrew Bailey as Co-Deputy Director of the FBI,” Bondi told Fox News Digital. “He has served as a distinguished state attorney general and is a decorated war veteran, bringing expertise and dedication to service. His leadership and commitment to country will be a tremendous asset as we work together to advance President Trump’s mission.”

Deputy Attorney General Todd Blanche echoed the praise in a social media post, writing: “Thrilled to welcome Andrew Bailey as our new FBI Co-Deputy Director. As Missouri’s Attorney General, he took on the swamp, fought weaponized government, and defended the Constitution.”

Traditionally, the deputy director is responsible for the FBI’s day-to-day operations. It remains unclear how Bongino and Bailey will divide those responsibilities under the new arrangement.

Bailey, who had been considered for the FBI director post before President Trump’s inauguration, interviewed at Mar-a-Lago late last year but was ultimately passed over after Trump said he wanted a more aggressive “legal bulldog” for the top job, CNN reported at the time.

Bongino’s future has been clouded since the reported bitter clash with Bondi over the Epstein files — a matter Trump himself sought to rein in.

In announcing his resignation as Missouri’s Attorney General, Bailey expressed gratitude and looked ahead: “My tenure as Attorney General has been the honor of my professional career, but what has made it truly meaningful has been the opportunity to serve my home state. Together, we have defended the rule of law and safeguarded our freedoms. I am forever grateful.”

He added in another statement, “I extend my deepest gratitude to President Trump and U.S. Attorney General Bondi for the privilege to join in their stated mission to Make America Safe Again.”

For his part, Bongino kept his reaction brief, posting a simple “Welcome” followed by three American flag emojis.

“The Fox reporting tonight is that Dan Bongino is effectively out. He’s had somebody else given his same job title, after he reportedly clashed with the White House and AG Pam Bondi over the administration’s efforts to suppress the material about Epstein that it holds in its own files,” MSNBC host Rachel Maddow said on Tuesday.

“The White House is apparently so unhappy with Dan Bongino’s job performance that they are quietly managing him out of the FBI,” Democrat strategist Max Burns claimed.

The White House has not indicated that Bongino is being removed from his position.