As the NYPD’s chief of department, Jeffrey Maddrey was the agency’s highest-ranking uniformed officer.

Now, he finds himself the target of multiple law enforcement agencies.

Thursday morning, FBI agents searched Maddrey’s home in southeast Queens. And the NYPD’s own Internal Affairs Bureau is also investigating, according to a statement from police commissioner Jessica Tisch.

“At my direction, the Internal Affairs Bureau of the New York City Police Department is working with law enforcement authorities to investigate allegations against former Chief of Department Jeffrey Maddrey,” the statement said. “Maddrey was suspended from the Department this morning, as law enforcement agents executed search warrants at several locations, including his residence.”

Maddrey had already submitted his resignation in late December, after he was accused by a former subordinate of sexual misconduct.

Lt. Quathisha Epps said Maddrey coerced her into an ongoing sexual relationship in exchange for overtime. Maddrey has denied the allegations, describing the relationship as a consensual office fling, and said Epps was seeking to deflect from her own abuse of the overtime system.

Epps was the NYPD’s highest-paid employee last fiscal year, earning more than $400,000, including more than $200,000 in overtime.

Maddrey, through his attorney, said he wasn’t responsible for approving her overtime and was prepared to litigate. “Now, without the constraints of the NYPD, he’s going to take the gloves off and fight for his good name going forward,” his attorney, Lambros Lambrou, said at a news conference last Friday.

Former NYPD Chief of Patrol John Chell was officially named Maddrey’s replacement this week.

Maddrey has long had the backing of Mayor Eric Adams, who defended him in the face of previous controversies — but has struck a slightly different tone in recent days.

“These are troubling allegations,” the mayor said during his weekly Q&A session with reporters Tuesday. “They're going to go through their review as they're supposed to do. And Commissioner Tisch is doing her review there. And I'm proud of what she's doing.”

Following news of the federal investigation, the office of Manhattan District Attorney Alvin Bragg said Thursday it has paused its own investigation into the claims against Maddrey.