The CMU was started on August 20, 2006 following an unsuccessful attempt to resolve deep divisions in the Muslim Canadian Congress (MCC) board.

The attempt failed when members representing one of the factions did not show up for the Board meeting called to resolve the differences and to elect a new executive.

The CMU has hosted a number of events including several mixed-gender woman-led Friday afternoon prayers and has co-sponsored a "Peace Iftar" with Salaam each Ramadan since 2006.

They have also partnered with other groups for various events such as public forums with Tariq Ali on October 15, 2006 and November 14, 2008.

The CMU also was one of many groups who presented a position statement to the Ontario Citizens' Assembly on Electoral Reform in 2007.