For the final two years of his playing career, Muscat served as a playing assistant coach under Ernie Merrick. Due to a clause in his contract with Melbourne Victory, which makes him an assistant coach at Melbourne Victory for the next two years after his retirement, Kevin Muscat began serving as an assistant coach at Melbourne Victory shortly after his retirement from football. After Mehmet Durakovic was sacked after a poor run of results, Muscat was appointed as the caretaker coach of Melbourne Victory until he was succeeded by former Ipswich Town and Queens Park Rangers manager Jim Magilton. In his only game as Victory manager, Melbourne Victory defeated the Newcastle Jets 2–1, with two own goals from defender Byun Sung-Hwan.