The estranged husband of missing Connecticut mom Jennifer Dulos allegedly had her body in a pickup truck, his girlfriend claimed — leading to his arrest Wednesday on a new tampering with evidence charge.

Michelle Troconis, the girlfriend of Fotis Dulos, 51, told Connecticut State Police that he had the vehicle washed “because the body of Jennifer at some point was in there,” according to an arrest warrant.

Police said they found a “blood-like substance” inside the truck and that it tested positive for Jennifer’s DNA, according to the 38-page warrant.

Troopers took the real estate developer into custody Wednesday, and he was released that afternoon on $500,000 bond.

Police say they believe Fotis was “lying in wait” for Jennifer at her New Canaan home the morning of her May 24 disappearance.

A photograph taken that day by a residential security camera is included in the warrant and is believed to be the last known picture of her.

It apparently shows the 50-year-old mom of five arriving home in her SUV at about 8:05 a.m. after having dropped off her children at school.

Police have said they found bloodstains on the floor inside her home and garage and believe Jennifer was the victim of “a serious physical assault.”

“The crime and the cleanup are ­believed to have occurred between 8:05 a.m. and 10:25 a.m.,” the warrant states.

At 10:25 a.m., Jennifer’s Chevy Suburban was seen being driven away from her home and cops believe Fotis Dulos was at the wheel of the vehicle, “carrying the body of Jennifer Dulos and a number of other items associated with the cleanup,” the warrant said.

A Toyota Tacoma pickup belonging to Fotis’ employee was spotted 100 feet away from where cops eventually found Jennifer’s abandoned SUV. It appears that Fotis had borrowed the truck, according to the warrant.

The employee, who was cleared as a suspect, allegedly told cops Fotis urged him to replace the truck’s seats and was “pushy” about it, sometimes growing angry.

Eventually the seats were removed, but the employee kept them “in the event they may be needed by police,” according to the warrant.

The worker told cops that Fotis had the interior of the pickup detailed and the exterior washed, the warrant said.

Fotis allegedly told the employee he was worried cops would find “a hair” belonging to Jennifer inside the truck because he’d apparently hugged her on Mother’s Day.

It’s not clear at what point the body allegedly might have been put in the pickup, but when cops asked Troconis why Fotis had it cleaned five days after Jennifer vanished, she allegedly replied, “Well obviously … it’s because the body of Jennifer at some point was in there,” the warrant said.

Fotis and Troconis, 44, were charged in June with tampering with evidence and hindering prosecution. They pleaded not guilty.

Those charges stemmed from surveillance footage that authorities said showed the pair dumping several trash bags containing items soaked with Jennifer’s blood.

Fotis’ attorney, Norm Pattis, tried to minimize the significance of the new warrant, calling it “unnecessary.” He said his client would be pleading not guilty at his next hearing, next Thursday.

“Apparently, Michelle has changed her tune and a handyman [who worked for Fotis’ real estate development company] is telling tales to deflect attention from himself,” Pattis said.

“We wish the State Police spent more time looking for Jennifer and less trying to build a case against Fotis.”

As he was released, Fotis told local outlets, “It’s an exhausting fight; I love my children. That’s about it.”