Colby had a change of head coach in 2004 when Tom Austin retired and long-time assistant coach Ed Mestieri took over. Mestieri has guided the Mules to a 13-3 record in his first two seasons, and Colby was second in all of New England in 2005. Mestieri was named Division II/III Coach of the Year by the Gridiron Club of Greater Boston after the 2005 season.

Tom Austin led Colby to a 24-11-1 record in Colby-Bates-Bowdoin (CBB) games and won or shared part of 12 CBB titles. Austin was named Division II/III Coach of the Year by the Gridiron Club of Greater Boston and NESCAC Coach of the Year after leading the Mules to the New England Small College Athletic Conference title in 2000. He was honored as C Club Person of the Year in 2001.

Running back Aaron Stepka '05 became Colby's first All-America selection in football in 2002. He broke the NESCAC single-season rushing record with 1,370 yards and led NCAA Division III in rushing with 171.2 yards per game. Stepka broke the Colby single-season rushing record as well in 2002. The old record was held by Peter Gorniewicz '75, who gained 1,170 yards during Colby's 7-1 season in 1972 under head coach Dick McGee.