After commissioning, "Cowichan" transferred to the east coast, arriving in September 1941. She worked up at Bermuda and upon her return, was assigned to the Halifax Local Defence Force for local patrol and minesweeping duty. In January 1942, she transferred to Newfoundland Force. "Cowichan" was assigned to escort group 4.1.17 alongside the destroyer , corvettes , , and Free French and . From 29 December 1941 to 11 January 4.1.17 escorted convoy SC 62, handing the convoy over to the British escort group B7. From 17 January to 28 January the group escorted convoy ONS 56. From 6–15 February the group escorted convoy SC 68. In September the ship was ordered to join the Western Local Escort Force (WLEF), the command charged with escorting convoys along the coast of Canada and into the United States. In early 1942, the ship's main fans were sabotaged during repairs at St. John's. The resulting investigation was faulty and was closed quietly. This was one of the first recorded attempts of crew sabotage in Royal Canadian Navy history. In January 1943, "Cowichan" was assigned to a WLEF escort group 24.18.7 with destroyer and corvettes and .