In 2009–10, Dineen was hired as an assistant coach with the Toronto Marlies, the AHL affiliate of the Toronto Maple Leafs. He remained with the Marlies as an assistant under head coach Dallas Eakins from 2009 to 2013 and under Steve Spott in 2013–14. Dineen was promoted to head coach of the Marlies for the 2014–15 season, earning a record of 40–27–9–0 for 89 points, finishing second in the North Division. In the post-season, the Marlies lost to the Grand Rapids Griffins in the first round. The Maple Leafs then hired Sheldon Keefe as head coach of the Marlies for the 2015–16 season, deemed and up and coming coach, and Dineen was moved back to the assistant coaching position. Following the 2016–17 season, Dineen was not retained by the Marlies.