In 1942, Boettiger became concerned that he was not doing his part for the war effort. On inquiry, FDR declined to use him in diplomatic matters since he was in private business. In April 1942 Boettiger was given a leave of absence by Hearst and appointed a captain in the Army. He participated in the invasions of Sicily and Italy, served in Military Government, and was promoted to major in November 1943 and to lieutenant colonel shortly thereafter. As a liaison officer in the Military Government, he was ashore at Salerno during the first day of the landings.