Mooy was released by Western Sydney Wanderers on 21 May 2014, and was announced to have joined A-League rivals Melbourne City the same day. He scored his first goal against Brisbane Roar, and also scored in both fixtures against his former club Western Sydney Wanderers. At the end of the season he claimed Melbourne City's Player of the Year award and was the club's top scorer that season, also racking up eight assists. Mooy became the youngest ever marquee player in A-League history when he re-signed with Melbourne City for the 2015–16 season. On 29 September, he scored a hat-trick against Heidelberg United in the FFA Cup quarter finals with two of the goals coming from outside the box, and in doing this he also became the first ever City player to score a hat-trick in the FFA Cup. During his time with Melbourne City, Socceroos manager Ange Postecoglou labelled him the "best and most exciting player in the A-League", while former Socceroo goalkeeper Mark Bosnich described him as "the best Australian midfielder playing anywhere in the world". Melbourne City were reported to have rejected a $2m offer for Mooy from Saudi Arabia club Al-Nassr. On 5 March 2016, he assisted Bruno Fornaroli for two of his three goals to move to 20 assists for the season; an all time A-League record.