Chen signed with the Atlanta Braves as an amateur free agent on July 1, 1993. He made the South Atlantic League All-Star team in 1997 when he went 12-7 with a 3.51 ERA in 28 starts for the Macon Braves. In 1998 he made 23 starts for the Greenville Braves and was 13-7 with a 3.29 ERA. He was selected by the Southern League as an All-Star and the Most Outstanding Pitcher. He was also a Double-A All-Star, Baseball America minor league All-Star and the Braves minor league pitcher of the year.