From 1999 to 2013, Matthews was the head coach at James Madison University. The team had gone 3–8 in the year before, but Matthews turned them around that season and led them to an 8–4 record, an Atlantic 10 Conference title, and the school's first postseason appearance since 1995. Matthews won the Eddie Robinson Award that year, annually given to the top head coach in NCAA Division I-AA football. Five years later, after failing to make the postseason four years in a row, the Dukes finally made the playoffs again. They became the first team to win three straight road games on the way to an NCAA Division I-AA Football Championship, defeating the Montana Grizzlies, 31–21, in the 2004 Championship Game. The Dukes made the playoffs again in 2006 and 2007, losing in the first round each time. On February 25, 2008, amidst rumors that he might leave James Madison to help start the football program at the University of South Alabama, Matthews signed an extension with JMU to coach through the 2012 season.[4] On September 27, 2008, JMU beat University of Maine 24–10, earning Matthews his 68th career win at JMU to become the school's all-time winningest coach.[5] On November 22, 2008, the Matthews led Dukes defeated Towson University to finish conference play undefeated, winning the CAA outright and qualifying for their third straight FCS playoff appearance. On January 7, 2010, Matthews signed a one-year extension to his contract which extended through the 2013 season.[6] During the 2012 season, Matthews gained his 100th career win in a hard-fought, 13–10 victory against conference foe Towson.[7]
On November 25, 2013, JMU athletic director Jeff Bourne announced that Matthews had been fired.[8] This came after the Dukes finished the 2013 season 6–6 and missed the FCS playoffs for the fourth time since advancing to the NCAA Semifinals in 2008.
2010 Virginia Tech victory
On September 11, 2010, the Dukes upset then No. 13 Virginia Tech, 21–16 in front of 66,233 at Lane Stadium in Blacksburg. James Madison became the second NCAA Division I Football Championship Subdivision (FCS) team in college football history to knock off a ranked NCAA Division I Football Bowl Subdivision (FBS) opponent, following Appalachian State, which upset No. 5 Michigan in 2007.[9] Later that season the Hokies went on to win the ACC Championship and finished ranked #15, making the JMU upset even more remarkable, especially considering that the Dukes finished the season with a 6–5 record (5–5 against FCS competition). After the game, Matthews referred to the victory as "the biggest win in my professional career"—even bigger than the 2004 national championship.[10]
Later coaching career
After his firing, Matthews joined Coastal Carolina as defensive coordinator in 2016. On December 7, 2017, he announced his retirement from coaching.[11]