Maciocia returns to the Alouettes, where he began his professional coaching career in 1996 as a Quality Control Coach. He rapidly climbed the ladder and was the team’s Offensive Coordinator by 2001, before taking on the same responsibilities with the Edmonton Eskimos from 2001 to 2004, helping the team engrave its name on the Grey Cup in 2003.
The Eskimos then appointed him as the Head Coach, in 2005. On top of becoming the first Quebec-born head coach in CFL history, he hoisted the Grey Cup in his first season in that role, following a dramatic overtime win against the Alouettes. He was then handed the General Manager duties in 2007. In November of 2010, he was named Head Coach of the Université de Montréal Carabins and, in November 2014, at Percival Molson Memorial Stadium, home of the Alouettes, Maciocia led the Carabins to their first Vanier Cup championship, making him the first ever Head Coach to win both the Grey Cup and Vanier Cup.
In nine seasons on the other side of Mount-Royal, Maciocia maintained a 57-16 record while leading the team to three Dunsmore Cup championships. On those three occasions, the Carabins went on the Vanier Cup championship game. At Université de Montréal, Maciocia, who was decorated by the Quebec National Assembly in 2005, guided many players who eventually made their way to the CFL, including Antoine Pruneau, Byron Archambault, current Alouettes defensive end Jean-Samuel Blanc, as well as David Foucault, who also played in the NFL. He was elected the 2016 coach of the year in the RSEQ.