In 1942, while America geared up for front line involvement in World War II, Pflueger received fewer assignments than he had been seeing previously. Grover Magnin kept a flow of work with I. Magnin designs, and Pflueger also helped the Army with a depot building in Ogden, Utah. He began to draw up plans for a 12-story cross-shaped medical teaching hospital for the University of California, San Francisco (eventually to be built at 505 Parnassus in 1955 with additional design work performed by his brother Milton Pflueger). His firm accepted a commission to excavate below the Mark Hopkins Hotel in order to create a bomb-resistant radio transmission center for AM station KSFO and shortwave programs of the Voice of America. This space became the hotel's underground parking garage after the war.