Gilkey came to New York from the St. Louis Cardinals in a trade for three minor league players on January 22, 1996. In '96, he led the Mets with 117 RBIs to tie a team record. Bernard's 44 doubles and .393 on-base percentage were also team highs for the season. In addition, he had 30 homers and a .317 batting average.
In his first game as a Met, he homered against his former St. Louis team in the Mets' 7-6 Opening Day win on April 1 at Shea Stadium. At Shea on May 26, Bernard slugged a homer for the only run of a 1-0 Mets victory over the Padres. Three times in '96, Gilkey hit two homers in a game. On May 28, he connected twice in the Mets' 4-0 win over the Giants. At Colorado on July 24, Bernard had two homers in a 7-6 loss to the Rockies. In the first game of a doubleheader on July 30, Gilkey homered in his first two at bats in a 5-4 Mets victory over the Pirates at Shea. Against Pittsburgh one day later, he homered to tie the game in the ninth inning in an eventual 3-2 Mets win in 10 at Shea.
Although he did not match his '96 production, Bernard still had an impressive season in 1997. He had 129 hits for the year (including 31 doubles and 18 home runs) and was a National League co-leader with 12 sacrifice flies. Gilkey had a run-scoring double in the Mets' 10-2 victory over the Reds at Shea on April 23. He slugged a two-run homer in a 6-0 Mets triumph over the Marlins at Shea on June 5. At Shea on July 19, Bernard hit a three-run homer in a 5-3 Mets win over the Reds. One day later, he slugged the 4,000th homer in Mets history in the team's 10-1 romp over the Reds at Shea. In a game against the Giants at Shea on August 27, Gilkey had a double, three singles and a sacrifice fly in the Mets' 15-6 victory. He hit a three-run homer in the 11th inning to give the Mets a 9-6 win over the Expos on September 13 at Shea. At Philadelphia on September 15, Bernard hit two homers and drove in the winning run with a tenth-inning single in a 10-5 Mets triumph over the Phillies in the first game of a doubleheader. He also singled twice, doubled and drove in two runs in a 7-3 Mets win over the Marlins at Florida on September 20.
Gilkey played 82 games for the Mets in an injury-plagued 1998 season. He had 60 hits during his time with the team for the year. At Cincinnati on April 19, Bernard singled, doubled twice, drove in three runs and scored five times in the Mets' 14-0 win over the Reds. He also singled, doubled and homered in a 9-2 Mets victory at Boston on June 5.