Although Bowman was drafted by the Mets in the 12th round (357th overall) in the 2002 Major League Baseball Draft, they failed to agree upon a contract in time for him to play during the 2002 season. Bowman would begin his professional career during the 2003 season when he spent time with both the Kingsport Mets and the Brooklyn Cyclones. He went on to have a successful 2004 season playing for the Capital City Bombers where he hit .258, had 19 home runs and 69 RBIs in 116 games played. However, he began to develop chronic back problems during the 2005 season while playing for the St. Lucie Mets of the Florida State League, and was only healthy enough to play in 125 games from over the next three seasons.