Ochoa was acquired by the Mets in a trade with the Baltimore Orioles on July 28, 1995. He made his Mets premiere with a pinch-hit single in his first major league at-bat on September 18 at Atlanta. Alex also had two singles and a double in the Mets' 5-4 win over the Reds in a doubleheader opener at Shea Stadium on September 27.
In 1996, Ochoa batted .294 with 4 homers and 33 runs batted in. He had 19 doubles and 37 runs scored during the season. On June 28, Alex got three hits and scored twice in the Mets' 7-2 win at Houston. He hit for the cycle in a 10-6 Mets victory at Philadelphia on July 3. At Montreal on July 6, Ochoa hit a three-run homer in the Mets' 11-3 rout of the Expos. He also went 15-for-44 (.341) during a 12-game stretch from September 10 to September 26.
Ochoa played in 113 games for the Mets in 1997. He had 58 hits for 83 total bases for the year. Alex had a run-scoring single that put the Mets ahead to stay in a 4-1 victory at San Diego on April 3. He singled three times and scored two runs in the Mets' 5-0 win over the Dodgers at Shea on April 15. Ochoa got three singles in a 5-3 Mets win in 10 innings at Montreal on April 27. He singled, doubled and homered against the Red Sox on June 13 in the Mets' first regular season interleague game ever. At Shea on September 10, Alex went 4-for-4 with 3 RBIs in the Mets' 10-2 victory over the Phillies. He also had three singles, a run scored and an RBI in a 10-5 Mets win over the Phils in 10 innings in a doubleheader opener at Philadelphia on September 15.
On December 12, 1997, Ochoa was traded to the Minnesota Twins for Rich Becker. He continued to play in the major leagues over the next five seasons. Alex concluded his major league career with the World Champion Anaheim Angels in 2002.