A highly-touted pitching prospect in the Braves farm system, Chen was expected to team with lefty Odalis Perez to succeed Tom Glavine, John Smoltz, and Greg Maddux as the next generation of dominant Atlanta starters. Pleased with Chen’s progress in Double-A, the club had no qualms about trading Denny Neagle before the 1999 season, assuming that the 24-year-old Panamanian would make the rotation by the middle of the season. But despite his success in the minors, Chen didn’t impress as a spot starter, and in July 2000, with Atlanta looking for established pitching help for the postseason stretch, he was dealt with a minor leaguer to the Philadelphia Phillies for Andy Ashby.
Chen was a full-fledged starter for the rest of 2000, and ended up with hopes of being the first or second starter the following year. But while the rest of the 2001 Phillies staff enjoyed moderate success, Chen suffered. After a 4-5 record and 5.00 ERA at the beginning of July, he was sent down to Double-A for retooling, and then traded with a minor league pitcher to the New York Mets for relievers Turk Wendell and Dennis Cook.