Looking to improve the bullpen after the struggles of the 2008 season, the Mets signed closer Francisco Rodríguez to a three-year, $37 million contract on December 10, 2008.

Despite an injury depleted roster, the Mets finished May with a 19–9 record and trailed the Philadelphia Phillies by a half game for the NL East lead.

After finishing April and May with a combined record of 28–21,[5] injuries hurt the Mets in June and they went 9–18,[5] their worst month since September 2003, but lost only 2+1⁄2 games in the standings, as the Phillies were having their own struggles.

[6] On August 23, the Mets became the first team in National League history to fall victim to a game-ending unassisted triple play, turned by Eric Bruntlett of the Philadelphia Phillies at Citi Field in the bottom of the 9th inning.

Including Santana, the Mets' had 20 players see time on the Disabled list at some point during the 2009 season, including David Wright, John Maine, Jon Niese, Fernando Nieve, J. J. Putz, Billy Wagner, Brian Schneider, Carlos Delgado, Ángel Pagán, Gary Sheffield, Óliver Pérez, Ryan Church, Ramón Martínez, Jose Reyes, Alex Cora, Carlos Beltrán, and Fernando Martinez.

[5] However, second-half turnarounds of Francoeur and Daniel Murphy helped the Mets finish the season with the best batting average in the National League, tied with the Los Angeles Dodgers.