He was one of several founding members of several secular organizations such as the Centre for Inquiry Canada in 2007, where he served as National Executive Director until 2011.
He also founded the Freethought Association of Canada, which created the 2009 atheist bus campaign where Trottier served as one of the spokespersons.
The organization successfully lobbied for the secularization of the University of Toronto's graduation ceremony through the removal of convocation prayers.
Trottier's Canadian Campaign for Free Expression sparked the Centre for Inquiry's annual Blasphemy Day.
Atheist Alain Simoneau and the secular rights organization Mouvement Laïque Québécois had initiated an action before the Quebec Human Rights Tribunal (Commission des droits de la personne et des droits de la jeunesse) against Jean Tremblay, Mayor of the Quebec town of Saguenay, calling for an end to the practice of the municipal council initiating its city council meetings with a Catholic prayer, on the basis that doing so infringes on freedom of conscience and religion.
During his leadership he acted as one of the primary spokespersons for the 2009 Canadian Atheist Bus Campaign, which received considerable media attention.
[8] In 2010 Trottier was the skeptical voice on the pilot episode of The Conspiracy Show with Richard Syrett, airing on VisionTV.
"[11][better source needed] Since January 2011, Trottier has appeared regularly on the John Oakley Show's Tuesday morning Culture War segment on Toronto Talk Radio AM640.
[12] His debate opponents have tended to be conservative religious leaders, including Reverend Charles McVety, Pastor Scott Masson, and Rabbi Mendel Kaplan.
[21][27] The centre opened in downtown Toronto in August 2014, with programs including grief counseling, sexual trauma support, anger management, suicide prevention, fathering, tutoring and mentorship.