During World War II, the fort served as a control center for Boston Harbor's south mine field, a precaution taken in anticipation of potential attacks by Kriegsmarine U-boats. At that time, Fort Warren was garrisoned by the 241st Coast Artillery Regiment (Harbor Defense), a Massachusetts National Guard unit that was federalized in September, 1940. As new 16-inch batteries were built, particularly Battery Murphy at the East Point Military Reservation, Fort Warren's remaining guns were scrapped in 1942–1944. Fort Warren was permanently decommissioned after 1950. At some point an emplacement of Battery Bartlett was demolished for an access road.