After graduating from the Theatre Arts Program at George Brown College in 1989, Michael Mahonen auditioned for a young company formed for The Citadel Theatre in Edmonton. His first job as a professional actor involved the role of James Keller in "The Miracle Worker," as well as the roles of Lucius and Popilious Lena in "Julius Caesar."

In 1990 he was chosen for the role of Gus Pike for the CBC television program Road to Avonlea. He garnered three Gemini Award nominations in 1993, 1994 and 1995 for his work on the television series. In 1992, he starred as a jazz trumpet player with Billy Dee Williams in the film Giant Steps. He then played Lee Colgan in the CBC miniseries Conspiracy of Silence directed by Frances Mankiewicz.

In the summer of 1994 he played the role of Jacob Mercer in "Salt Water Moon". This was part of David French's Mercer family saga set in Newfoundland.

He also guest starred in numerous American and Canadian television projects including an episode of Star Trek: Voyager entitled "Nemesis", in which he played a humanoid named "Brone." In 1997, Michael Mahonen starred in Judith Thompson's "Sled" at Toronto's Tarragon Theatre. He then returned to film, co-starring in the 1998 film "Captured". He went on to make several more films including "Blindness" (2008).

In 2003, Michael began work on his first feature film "Sandstorm". The film involved a fact-based drama about the persecution of Falun Gong practitioners in China. He wrote, directed and produced the entire film for under $5,000. The cast was made of volunteers. The film received 29 awards including Best Feature Film, Best Drama, Best Director and Best Screenplay.