A versatile infielder, Michael Parker was originally drafted by the New York Mets in the 24th round of the 2007 June first year player draft from George Washington University. For the Colonials in 2007, Parker was named a third team All-American by Louisville Slugger and Collegiate Baseball Magazine. He was a member of the 2007 Atlantic 10 All-Conference first-team, batted .373 with 60 RBI, 22 doubles and 10 home runs. Overall, he ranked in the league's top-five in eight separate offensive categories. In his last season at GW, he finished first on the team in slugging percentage (.604), on-base percentage (.434) and hits (84) and was second in home runs.

He made his professional debut with Kingsport (TN) of the Appalachian League where he was named team MVP, batting .298 with seven doubles, four home runs, 19 RBI, and seven stolen bases for the K-Mets. He was also named the Appy League player of the week for the week ending August when he batted .467 (7-15), with six runs scored, two home runs, five RBI, seven walks, three SB, and a .867 Slugging Percentage. He appeared in six games at second base, four games at third base, 15 games at shortstop, and 19 games in the outfield.

He split the 2008 season between Brooklyn of the New York-Penn League and Savannah of the Class A South Atlantic League. He appeared in 67 games for the Sand Gnats hitting 11 doubles, one triple, three home runs and 28 RBI. He appeared in 19 games at second base, one game at third base, and 35 games in the outfield.