In , Trachsel recovered to start 30 games and tied Tom Glavine for the team lead with 15 wins, despite an earned run average near five. On September 18, 2006, he had one of his best performances of the season as the Mets clinched the National League Eastern Division Championship. He pitched innings, allowing three hits and three strikeouts in the 4-0 win over the Florida Marlins. He also started the clincher of the NLDS, but was shaky and removed in the 4th inning. In Game 3 of the NLCS, he gave up five runs in just one inning before being hit by a hard ground ball. The Mets lost the game 5-0.