Mahomes was signed by the Mets in December 1998. He went 8–0 in the 1999 season during 39 relief appearances, and helped the Mets reach the playoffs. Mahomes made four relief appearances during the postseason, recording a 2.25 ERA in eight innings pitched while striking out four, as the Mets lost to the Atlanta Braves in the NLCS. In 2000, Mahomes was 5–3 in 53 appearances (five starts), and while the Mets reached the 2000 World Series, Mahomes was left off the Mets' playoff roster. In his two seasons with the Mets, Mahomes appeared in 92 regular season games (five starts) with a 4.74 ERA, 13–3 record, and 127 strikeouts in innings. He became a free agent in December 2000.