World War II, 1944–1945

Between 29 October and 5 November 1944, Manitowoc steamed to Boston, Massachusetts, where she was placed out of service on 8 November and converted by the Boston Navy Yard for use as a weather patrol ship. She was then recommissioned at Boston on 5 December, with Lieutenant Commander J. A. Martin USCG commanding and underwent shakedown off Bermuda during late December 1944 and early January 1945. After returning to Boston on 20 January 1945, she joined Escort Division 34 for duty as a weather ship in the North Atlantic.

Departing Boston on 2 February, she reached NS Argentia, Newfoundland on 5 February and the following day undertook her first weather patrol. She relieved the Woonsocket (PF-32) on 8 February and began patrolling her assigned station. Equipped with specialized radio transmitters and meteorological equipment, she spent two weeks transmitting valuable weather data as the Allies began their final push to defeat Nazi Germany. She was relieved on 24 February, returning to Argentia by 26 February.

Before the end of the war in Europe, the Manitowoc made two further weather patrols in the North Atlantic, carrying her from Newfoundland as far east as Iceland. She also helped deter the remnants of the Kriegsmarine submarine fleet from action by patrolling the sea lanes in her area.

Post-war operations, 1945–1946

After the end of the war in Europe, Manitowoc continued to patrol the North Atlantic, serving primarily as an air-sea rescue ship. Between 29 May 1945 and 10 February 1946 she completed seven such patrols. During a patrol in late July, she provided medical aid for the Panamanian merchantman SS Yemasee and on 2 August her medical officer performed an emergency appendectomy on a crewman from the Swedish merchant ship SS San Francisco.

Manitowoc returned from her final patrol on 10 February 1946 and was decommissioned at Boston on 14 March 1946.