Following his playing career, Bhonapha was offered a graduate assistant position at his alma mater Hawaii by head coach June Jones, where he helped to coach the defensive backs with secondary coach Rich Miano.[3] While at Hawaii, he was credited with connecting Davone Bess with Hawaii, as the two had the same high school football coach.[4]
Boise State
Bhonapha was hired as the director of football operations at Boise State in 2006. He was reassigned to running backs coach in 2009 in a series of staff shuffling made by Boise State head coach Chris Petersen.[5] He added the title of recruiting coordinator in 2011.
Washington
Bhonapha followed Petersen to Washington in 2014 to serve as his running backs coach and the program's recruiting coordinator.[6] While he was the recruiting coordinator, he and fellow assistant Ikaika Malloe were credited with rebuilding a recruiting pipeline in the state of Hawaii in part to their connections to the state that ended up with the successful recruitments of players such as Zion Tupuola-Fetui.[7] He was promoted to special teams coordinator in 2021 following the promotion of Bob Gregory to defensive coordinator.[8]