Stahr served as Secretary of the Army in 1961 and 1962, during the Berlin crisis and the Central Intelligence Agency-sponsored Bay of Pigs invasion, aimed at ousting Fidel Castro from power. A major reorganization plan was launched; combat division structure was reorganized, special warfare forces community relations (Civic Action) were expanded, and the Army was strengthened during the Berlin Crisis. Stahr also mobilized the Alabama National Guard in 1961, when the Kennedy Administration undertook desegregating of the University of Alabama.