In his 24 years at Appalachian State, Moore posted a losing season only once. He led his 2005 Mountaineers team to the NCAA Division I-AA Football Championship. This was the first national championship for any college football team in the state of North Carolina. Moore and the Mountaineers repeated as champions in 2006 and 2007, achieving the first "three-peat" in NCAA Division I FCS/I-AA history. Moore was forced out as head coach at the conclusion of the 2012 season. He was selected for inclusion into the Southern Conference Hall of Fame, and College Football Hall of Fame in 2014.