After training exercises with submarines off New London, Cowie sailed on escort duty, screening two convoys to Casablanca between 12 December 1942 and 28 April 1943.

Cowie was one of those response to calls for fire support broke up the counterattack by German tanks against the 180th Regimental Combat Team on 11 July.

She made 18 transatlantic voyages to United Kingdom and Mediterranean ports until 5 May 1945, when she entered Boston Navy Yard for conversion to a high-speed minesweeper; Cowie was reclassified DMS-39 on 30 May 1945.

Sailing from Boston 24 June 1945, Cowie joined in minesweeping exercises at Norfolk until 18 July when she departed for San Diego, arriving 3 August.

Sweeping mines in the Yellow Sea and off Kobe and Wakayama, Japan, Cowie remained in the Far East until 25 March 1946 when she departed Yokosuka for San Francisco, arriving 11 April 1946.