Wendell was acquired by the Mets in a six-player trade with the Cubs on August 8, 1997. He made 13 relief appearances over the remainder of the '97 season. On September 2, Turk recorded a save in the Mets' 8-5 win over the Blue Jays at Shea Stadium.
In 1998, Wendell had a 2.93 earned run average and a 5-1 won-lost record. He also recorded 58 strikeouts in 76 and two-thirds innings pitched. On March 31, Turk pitched two scoreless innings and got the win in the Mets' 1-0 season-opening victory over the Phillies at Shea. He also recorded a victory with two shutout innings on April 4 at Shea as the Mets defeated the Pirates, 7-6, in 13 innings. Wendell was the winning pitcher in a 9-8 Mets triumph over the Giants at Shea on August 6. At Houston on September 16, he struck out the side in order in the 11th inning for a save in the Mets' 4-3 victory over the Astros.
Wendell set a record for Mets pitchers with 80 game appearances in 1999. He had five wins and three saves in the team's National League Wild Card season. Turk recorded victories at Colorado on September 13 (6-5) and September 15 (10-5) during the Mets' drive to the title. He was the winning pitcher in Game 1 of the National League Division Series as the Mets came away with an 8-4 triumph at Arizona on October 5. Wendell also got credit for the victory in the Mets' 3-2 win over the Braves in Game 4 of the National League Championship Series on October 16 at Shea.
In the 2000 pennant-winning season, Wendell again led all Mets pitchers in appearances with 77. He had 8 wins and 73 strikeouts during the year. At Shea on April 20, Turk got the win in the Mets' 5-4 triumph in 10 innings over the Brewers. He hurled a perfect ninth inning for the win in a 7-6 Mets victory over the Diamondbacks at Shea on May 21. Wendell pitched four innings of relief to record a victory as the Mets defeated the Rockies, 13-2, at Shea on August 17. He came out with a win on September 5 in the Mets' 3-2 10-inning victory at Cincinnati. In Game 2 of the National League Championship Series, Turk was the winning pitcher as the Mets defeated the Cardinals, 6-5, at St. Louis on October 12.
In 2001, Wendell had a 4-3 won-lost record in 51 and one-third innings pitched for the Mets. He also struck out 41 batters and posted a 3.51 ERA with the team. Turk had three strikeouts in three innings to record a save in the Mets' 8-0 win over the Dodgers at Shea on May 18. Against the Yankees on June 17, he got the win as the Mets made a late comeback for an 8-7 victory at Shea. Wendell got another victory at Shea one day later as the Mets defeated the Expos, 2-1. He also pitched one and two-thirds scoreless innings for the win in the Mets' 4-3 triumph over the Marlins in 11 innings at Shea on July 18.
Wendell and Dennis Cook were traded to the Phillies for Bruce Chen and Adam Walker on July 27, 2001. One day after the deal, Turk surrendered a home run to Robin Ventura in the ninth inning that gave the Mets a 4-3 win over Philadelphia. Wendell finished the '01 season and pitched in 2003 with the Phils. He ended his career with the Rockies in 2004.