In 2009, Davis started the year with the St. Lucie Mets. He began to turn it around, hitting .289 with 7 home runs in 59 games. He was then promoted to the Double-A Binghamton Mets, where he came into his own, hitting .309 with 13 home runs, 41 RBIs, and a .565 slugging percentage in half a season. Mako Oliveras, the B-Mets manager, described him by saying: "Very live bat; the ball jumps off his bat when he makes contact. And as for defense, he's like a vacuum cleaner." For 2009, Davis was named the Mets Organizational Player of the Year.
After the season the Mets assigned him to the Surprise Rafters of the Arizona Fall League, where he hit .391. He was named to the Arizona Fall League's all star Rising Stars Game. In September 2009, he played for the gold-medal-winning U.S.A. World Cup team. In the off-season, Baseball America rated him the Mets’ No. 4 prospect.