Colón was signed as an amateur free agent by the Atlanta Braves in 1995 and began his professional career with the Braves Dominican Summer League team in 1996. In 1997, he ranked first in the Gulf Coast League in runs allowed (47) and earned runs (30), 5th in innings pitched (63), 4th in hits allowed (68), 2nd in games started (12). In 1998, he ranked 3rd in the Appalachian League in runs (59) and games started (13), 4th in earned runs (47) and first in hits allowed (92) and losses (7).\n', '

In 1999, he was named by the organization as Jamestown\'s Pitcher of the Year. He led the team in wins and strikeouts and tied for the team lead in innings pitched. Colón missed all of 2000 with an injury. Healthy again in 2001, he was promoted to Macon on May 3 from extended spring training. He had the 9th best walks per 9 innings ratio in Macon Braves history (1.83) and struck out a season high 7 batters three times. He struck out 6 in 6 innings on May 18 at Asheville for his first win of the season.\n', '

He put together a solid season in 2002, going 9–8 with a 3.59 ERA. In the two seasons after his arm trouble, he walked just 64 batters in 291 innings with 185 strikeouts. Colón pitched a complete game on June 2 versus Frederick (9 IP, 7 H, 1 R, 1 ER, 6 K). He also struck out a season-high eight batters on May 6 vs. Winston-Salem (​7 1⁄3 IP, 6 H, 1 R, 0 ER, 1 BB, 8 K).\n', '

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