Ex-NYPD honcho Jeffrey Maddrey’s Queens home was raided by the feds Thursday as investigators probe salacious accusations he traded sexual favors with an underling for obscene overtime.

The probe by the Southern District of New York is centered on whether federal funds were misused to pay for the subordinate’s alleged stolen overtime, sources told The Post.

Maddrey — who resigned late last month as the NYPD’s chief of department — was suspended Thursday morning, Police Commissioner Jessica Tisch said in a statement revealing the investigation and the raids on Maddrey’s home and other locations.

“Maddrey was suspended from the department this morning, as law enforcement agents executed search warrants at several locations, including his residence,” she said, without specifying which other places were raided.

The NYPD’s Internal Affairs Bureau is working with law enforcement authorities on the probe, Tisch added, directing questions to SDNY.

Video obtained by The Post showed federal agents hauling boxes from Maddrey’s Rosedale house and taking photographs.

Maddrey had served as the NYPD’s highest-ranking uniformed officer. He abruptly put in his resignation papers, which has not yet gone into effect, on Dec. 20 after The Post uncovered explosive accusations that he demanded sexual favors from a subordinate in exchange for astronomical amounts of overtime.

He has admitted to having a “consensual, adult relationship” with Lt. Quathisha Epps, but denied her claims that he routinely preyed upon her and demanded sexual favors.

Epps had leveled the allegations against Maddrey in a complaint she filed against the city with the federal Equal Employment Opportunity Commission.

She alleged Maddrey engaged in “quid pro quo sexual harassment” by coercing her to “perform unwanted sexual favors in exchange for overtime opportunities in the workplace.”

Epps, who held an administrative post in Maddrey’s office, was the NYPD’s top earner in fiscal year 2024, payroll data show.

She raked in $400,000 that year, with overtime pay accounting for more than half, records show.

A deputy chief overseeing overtime in Maddrey’s office – Paul Saraceno – was placed on modified leave amid the scandal, The Post has also learned.

Chris Monahan, who heads the Captains Endowment Association union repping Saraceno, distanced the chief from the accusations.

“Usually commanding officers oversee overtime in a given command,” Monahan told The Post. “However, in this very unusual circumstance, the Lieutenant in question reported exclusively and directly to the chief of department who gave her assignments and authorized her overtime.” 

Epps, when contacted by The Post, referred questions to her attorney, who didn’t return a request for comment.

The Post also reached out to Maddrey’s lawyer, Lambros Lambrou, Thursday after the raids, but didn’t hear back.

NYPD cops are required to give 30 days notice before leaving the force for retirement, giving the agency time to wrap up loose ends, including pending internal investigations. The NYPD’s internal affairs bureau is tasked with making referrals to outside prosecutors, including the Manhattan US Attorney’s Office.

The same federal office was behind a spate of stunning raids on top officials in City Hall in September, and Mayor Eric Adams’ historic bribery and corruption indictment, to which he has pleaded not-guilty.

The raids Thursday were only the latest to hit an ally of Adams, who last week tried to distance himself from Maddrey – even as he defended the former police official’s checkered record.

The relationship between Maddrey and Adams goes back years, insiders said.

The mayor went to bat for Maddrey in the wake of a separate scandal involving a subordinate that resulted in a messy federal sexual harassment lawsuit in 2016.

The underling – a woman NYPD officer – accused Maddrey of pressuring her into a sordid sexual relationship. At one point, she pointed a gun at Maddrey after he allegedly attacked and choked her, according to the lawsuit.

Maddrey denied the accusations and the lawsuit was later dismissed, although the NYPD later docked him 45 vacation days for carrying on the affair, court papers state.

Adams afterward helped put Maddrey’s career on track to a top spot in the NYPD, insiders said.

Just days after Adams nabbed the win in the 2021 general election — and weeks before he named Keechant Sewell as police commissioner — Maddrey was loudly bragging to cops that he would soon be chief of the department under the new mayor, sources said.

As mayor, Adams continued to defend Maddrey after his pal allegedly interfered with the arrest of an ex-cop who pointed a gun at three teens in 2021.

The NYPD’s watchdog in 2023 found that Maddrey abused his authority, prompting Sewell to discipline him.

But Adams and high-level City Hall defended Maddrey, undercutting Sewell and partly leading to her departure.

“I think he handled it appropriately,” Adams said before the discipline decision. “I have the utmost confidence in Chief Maddrey.”

Last week, Adams contended Maddrey was involved in city government before his administration. He then defended Maddrey’s record leading the NYPD and argued past mayors have hired friends without controversy.

“His policing practices and what he has done as a police officer – the knowns: I have been extremely, extremely proud of those knowns,” Adams said. “Those are the things that people knew him for and what he has done.”

“You can’t predict unknowns,” he added. “And, you know, these are troubling allegations.”

One of Maddrey’s neighbors told The Post she hasn’t seen him since news of the scandal broke. 

“He’s a nice guy, but you don’t see the inside of a person,” she said. “They can be nice outside, but deep inside you don’t know what’s going on. When you’re in a certain position, you really shouldn’t get involved in certain situations. It’s ugly.”

– Additional reporting by Reuven Fenton and Emily Crane