When German stepped down in 2006, both German and most senior players favoured Monaghan to take over as senior coach, but the club board instead chose Scott Watters.
In 2007 and 2008, Monaghan joined the Fremantle Football Club in a development role.
He was appointed senior coach of West Perth for 2009, taking the team to the finals in his first year.
Days after leading West Perth to the 2018 WAFL Grand Final, which they lost to Subiaco, Monaghan was sacked as West Perth's coach.
He then took the vacant head coaching position at East Fremantle,[2] where he led the Sharks to victory in the 2023 WAFL Grand Final, breaking a 25-year premiership drought.