JEF United Ichihara Chiba
On 7 January 2012, Magilton was signed as head coach of A-League club Melbourne Victory for the remainder of the 2011–12 season, following the dismissal of Mehmet Durakovic. He took over from interim head coach Kevin Muscat after Melbourne Victory's home game on 7 January 2012 against the Newcastle Jets. Upon being appointed the new coach of Melbourne Victory, Magilton immediately went to work strengthening the squad, signing Australian international defender Mark Milligan on loan from JEF United Ichihara Chiba, Hong Kong based Spanish midfielder Ubay Luzardo on loan from Kitchee SC, and Sierra Leonean-Australian midfielder Julius Davies. In his debut match as Melbourne Victory's coach, Melbourne Victory drew 1–1 with Adelaide United. His first win as coach came in round 19, as Melbourne Victory defeated the Central Coast Mariners 2–1. After a lacklusture tenure as coach, in which the Victory recorded 2 wins, 5 draws and 5 losses in 12 games, the Victory failed to make the finals, causing Magilton to state that the club needed to rebuild the squad and change its culture. He went about attempting to achieve this goal by releasing defender Fabio Alves and veterans Tom Pondeljak and Rodrigo Vargas and signing Gold Coast United defender Adama Traoré and Central Coast Mariners defender Sam Gallagher.