From 2004 to 2009, he compiled a 26–34 record as head football coach at Cornell University.
Duke
On December 28, 2009, Knowles was named the defensive coordinator at Duke under head coach David Cutcliffe. Knowles had previously served as linebackers coach under Cutcliffe while he was head coach at the University of Mississippi (Ole Miss) in 2003.[2]
Oklahoma State
On January 29, 2018, Knowles was hired as the defensive coordinator at Oklahoma State under head coach Mike Gundy,[3][4] and held the position through the 2021 season. During Knowles' time at Oklahoma State, the Cowboys' defense saw significant statistical improvements. After regressing in areas like opponent points per play and opponent yards per play during Knowles' first season,[5][6] Oklahoma State's defense improved in each of Knowles' next three seasons.[7][8][9][10][11][12] For the 2021 season, Knowles' defense finished top ten in areas such as opponent points per play,[13] opponent points per game,[14] opponent yards per play,[15] opponent yards per game,[16] opponent yards per rush attempt,[17] opponent rushing yards per game,[18] team sack percentage,[19] and sacks per game.[20]
Ohio State
Ohio State Buckeyes coach Ryan Day announced on December 7, 2021 that Knowles had accepted the defensive coordinator position for his team effective January 2, 2022.[21]