Beltran was dismissed amid Major League Baseball's investigation into the Houston Astros' sign-stealing practices in 2017. He was implicated in an MLB report as a person who had knowledge of the scheme.
MLB suspended former Astros general manager Jeff Luhnow and former manager A.J. Hinch Monday, before both were fired by the team. Boston Red Sox manager Alex Cora -- another Astros coach at the time of the scheme -- was fired Tuesday.
Mets chief operating officer Jeff Wilpon and executive vice president and general manager Brodie Van Wagenen met with Beltran Wednesday and Thursday before making the decision. Van Wagenen and Wilpon also met with the MLB Commissioner's office Wednesday in New York City to discuss Beltran's status.
"This was not an easy decision," the Mets said in a 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."
Beltran, 42, had a decorated playing career before spending his final season with the Astros in 2017. The nine-time All-Star and 2017 World Series champion was hired to manage the Mets in November.
"I'm grateful to them for giving me the opportunity, but we agreed this decision is in the best interest of the team," Beltrán said in a statement. "I couldn't let myself be a distraction for the team. I wish the entire organization success in the future."
Beltran was the only player implicated in the MLB report.
"Approximately two months into the 2017 season, a group of players, including Carlos Beltran, discussed that the team could improve on decoding opposing teams' signs and communicating the signs to the batter," the MLB report said.
Beltran worked in the New York Yankees front office before signing a three-year contract to manage the Mets. The Mets now need to find a new manager less than a month before spring training.