In 2004, Francis was named Minor League Player of the Year by both "Baseball America" and "USA Today", becoming the first player in Colorado Rockies organizational history to win either of the awards. He became the fourth player to be honoured in the same season by both publications, joining Andruw Jones (1995–1996), Rick Ankiel (1999), and Josh Beckett (2001). Combined between Double-A Tulsa and Triple-A Colorado Springs, Francis went 16–3 with a 2.21 ERA and .194 average against in 24 starts. He struck out 196 batters in 154.2 innings pitched, for a ratio of 11.4 per nine innings. He had more strikeouts than hits (108) and walks (29) combined.