In 2007 he began the year with the Sox big league team, playing ten games as a pinch hitter or late inning replacement at catcher. In mid May he was sent back to AAA Charlotte getting put on waivers in July. He was selected off waivers by the Baltimore Orioles returning to the big leagues as a September call up. He hit .111 in 27 at bats that season.
In December 2007 he signed with the New York Mets as a free agent. Molina would play just two games for the Mets, making his debut on April 26th, 2008. He was one of five catchers used by the Mets that season, including main back stop Brian Schneider (110 games), Ramon Castro (52 games), Raul Casanova (20 games) & Robinson Cancel (27 games).
Molina was behind the plate catching John Maine at Shea Stadium, in a 4-3 win over the Atlanta Braves. Billy Wagner would help out with the save. Molina singled off Tim Hudson in his first Mets at bat. He went 1-3 with a walk on the night. Four days later he made his second & last Mets start, going 0-4 in a 13-1 debacle of a loss to the Pittsburgh Pirates. He played out the rest of the year at AAA New Orleans batting just .206, he was granted free agency at the end of the year.
After spending 2009 in the minors, he played four games with the Boston Red Sox in 2010 & three games with the A.L. New York club in 2011. He was granted free agency in November 2012 after playing in their minor leagues.