After their success in 2006, there were high expectations for the Mets in 2007, and they started the season strong, compiling a 34-18 record through May 31. And although they played basically .500 ball through the summer, the Mets still had a seven game lead in September, with 17 games to go. The Mets, however, would lose 11 of their next 16, allowing the Philadelphia Phillies to tie them with three games left. The Mets lost to the Marlins 8-1 in the final game of the season, while the Phillies went on to win their final game 6-1 against the Nationals and clinch the NL East by one game. The Mets became first team in MLB history to blow a lead of seven or more games with only 17 games to play, and, by one analysis, it was the 2nd worst collapse overall in MLB regular season history. Despite the season ending collapse, Minaya announced that Randolph would remain as manager for the 2008 season.

On January 29, 2008, the Mets agreed to trade four minor league prospects, including outfielder Carlos Gomez and pitcher Philip Humber to the Minnesota Twins in exchange for two-time Cy Young Award-winning pitcher Johan Santana. He agreed on a six-year contract extension on February 1 worth $150.75 million, the highest amount ever for a pitcher on a long-term contract. The trade was finalized on February 2 when Santana passed his physical. With Santana on board, the Mets are once again considered to be favorites in the National League and a favorite to win the World Series.