He was undrafted in the 1995 AFL Draft, so he signed with the Williamstown Seagulls in the Victorian Football League (VFL), playing 19 games with them in 1996.
He was a handy small forward for the club, and was noted for his solid kicking and courage, as well as his ability to get the "hard ball".
His performances across half-forward, booting 20 goals, and his defensive pressure was important, with the journeyman winning a premiership medallion in Port Adelaide's 2004 flag-winning side.
Mahoney played well in 2006, winning the Power's leading goalkicker award with 29 goals and earning himself a promotion to the onfield leadership group for season 2007.
In September 2013, Mahoney was appointed Melbourne's General Manager - Football Operations by CEO Peter Jackson.