It was following an episode of avian influenza that occurred in British Columbia in 2004 that the partners of the Quebec poultry sector, jointly with the Ministry of Agriculture, Fisheries and Food of Quebec (MAPAQ) , the Canadian Food Inspection Agency (CFIA), the Union of Agricultural Producers, the Association of Veterinarians in the Animal Industry of Quebec and the Faculty of Veterinary Medicine of the University of Montreal, agreed to unite their efforts to provide the industry with an emergency measures plan.

Initially established as a committee in 2005, the EQCMA gradually evolved to become registered as a non-profit organization under the Companies Act, Part III, of the Quebec government in February 2009.