The Mets lost their rights to the Minor League Baseball affiliate Buffalo Bisons as their AAA team.

On November 7, 2012, the Mets and outfielder Jason Bay agreed to part ways, with the team buying out the $21 million remaining on his contract and releasing him.

On December 17, the Mets and the Toronto Blue Jays agreed to a deal sending 2012 Cy Young Award winner R. A. Dickey, Josh Thole and Mike Nickeas to Toronto in exchange for prospects Travis d'Arnaud, Noah Syndergaard, and Wuilmer Becerra and veteran catcher John Buck.

[1][2] On August 30, 2013, the Mets traded catcher John Buck and outfielder Marlon Byrd through the waiver process, to the Pittsburgh Pirates.

Fans and certain media members have been publicly criticizing Collins' moves in games, and his general managing presence, and repertoire.