Carlos Beltran stepped down as Mets manager on Thursday, The Post’s Joel Sherman confirmed.

It comes less than three months after appointing him manager and just days after MLB confirmed his involvement in the Astros’ cheating saga as a player in 2017. The Mets had been debating Beltran’s future since Monday and were conflicted on what to do, according to The Post’s Joel Sherman. Beltran met with Mets top officials on Wednesday night and again Thursday morning to find a path to salvage his job, but were unable to find a suitable path.

Beltran, 42, had been on shaky ground since the league revealed Monday that he played a pivotal role in the Astros’ sign-stealing scandal, as a player during the 2017 championship season.

“At a meeting this morning with Jeff and Brodie we mutually agreed to part ways. I’m grateful to them for giving me the opportunity, but we agreed this decision is in the best interest of the team,” Beltran said in a statement released by the team. “I couldn’t let myself be a distraction for the team. I wish the entire organization success in the future.”

Beltran was the only Astros player implicated in the report, which led Houston to fire general manager Jeff Luhnow and manager A.J. Hinch.

No players were punished.

On Tuesday, the Red Sox canned manager Alex Cora — who has not yet been punished by the league — as he was a bench coach with Houston in 2017 and helped orchestrate the cheating, which included a center field camera that helped decipher signs and relay them to Astros hitters.

MLB determined Houston illegally stole signs in 2017, including the postseason, as well as part of 2018.

In November, Beltran denied to The Post he illegally cheated: “I’m not concerned. There’s nothing illegal about studying your opposite team. We all have the same opportunity to look out for information and tendencies.”

He also said he was not “aware of that [center field] camera.”

Mets general manager Brodie Van Wagenen previously said he didn’t “see any reason why this is a Mets situation.”

But everything changed following MLB’s explosive findings.

“This was not an easy decision,” COO Jeff Wilpon and Van Wagenen said in a combined statement. “Considering the circumstances, it became clear to all parties that it was not in anyone’s best interest for Carlos to move forward as manager of the New York Mets. We believe that Carlos was honest and forthcoming with us. We are confident that this will not be the final chapter in his baseball career. We remain excited about the talent on this team and are committed to reaching our goals of winning now and in the future.”

The league suspended Luhnow and Hinch one season each, and Houston subsequently fired both. In addition, the franchise was fined $5 million and stripped of its first- and second-round picks for 2020 and 2021.

On Tuesday, the Red Sox canned Cora, who led Boston to its 2018 World Series win, for helping orchestrate the cheating as the Astros’ bench coach in 2017. MLB also is currently investigating the Red Sox for their possible use of electronics in 2018, and it is possible Cora could still be suspended.