The 2013 Metro Atlantic Athletic Conference baseball tournament was held from May 23 through 26. The top four regular season finishers of the league's teams met in the double-elimination tournament held at Arm & Hammer Park in Trenton, New Jersey. Canisius, the tournament champion, earned the conference's automatic bid to the 2013 NCAA Division I baseball tournament.
The top four teams were seeded one through four based on their conference winning percentage. They then played a double-elimination tournament. Canisius claimed the third seed over Siena by tiebreaker.
The following players were named to the All-Tournament Team.
Jesse Puscheck was named Tournament Most Valuable Player. Puscheck was a designated hitter for Canisius.