In January, the Mets avoided arbitration, signing Maine to a one-year, $2.6 million contract. Maine initially struggled coming off the shoulder surgery, posting a 5.40 ERA to go with a 1–2 record in four April starts. However, he bounced back in his six starts in May, going 4–1 with an ERA of 2.75, nearly half of his April ERA. After a poor start in June, he was placed on the 15-day disabled list due to arm fatigue. Maine would stay on the DL with arm fatigue and numerous setbacks for a long amount of time. He eventually came back in mid-September and was eased back into the rotation, going more than 5 innings only once. In his last start of the season against the Astros, he went 7.0 innings letting up one earned run with 7 strikeouts, with that encouraging start he gave the Mets more certainty that he can return to his '07 form in the 2010 season. He finished the 2009 season with a 7–6 win/loss record throwing 81.1 innings with an era of 4.43.