The “Top Chef” alums behind one of New York City’s hottest fried chicken joints have been eating up company profits — spending proceeds on a $135,000 apartment renovation and side projects like a Puerto Rico pop-up, according to a new lawsuit by their business partner.

James Beard Award finalists Jeff McInnis and Janine Booth opened Root and Bone in Alphabet City in 2014 — quickly drawing accolades and hour-plus wait times.

The chef couple own equal shares in the restaurant with partner Richard Freedman, who says he’s been frozen out of the business by the pair in a Manhattan Supreme Court suit.

McCinnis and Booth “have failed to account for over $286,000 in cash distributions” including $136,000 they used to renovate their apartment above the East 3rd Street restaurant, $85,000 for rent for their pad, and payments to a PR firm for outside ventures like the pop-up restaurant in Puerto Rico, the suit says.

McInnis, who appeared on the fifth season of Bravo’s “Top Chef,” also gave himself a $10,000 raise– even though “he spends little time at the Root and Bone restaurant,” according to court papers.

McInnis told The Post that Freedman “has made a mistake.”

“None of this is true,” McInnis said.

Booth did not return a call for comment.

Freedman is suing for access to the company’s books plus the return of the $286,000.