Due to the academic policies of the National Socialists in general, and specifically the Nationalsozialistischer Deutscher Dozentenbund (NSDDB, National Socialist German University Lecturers League) at universities, Joos departed academia in 1941. He became the chief physicist at Zeisswerke Jena, where he also participated on the management board. He remained there until shortly after the end of World War II, when, in September 1946, he was appointed as ordinarius professor of experimental physics and director of the physics department at the Technical University of Munich; he succeeded Rudolf Tomaschek, who had been suspended. For the academic years 1947 to 1949, Joos was visiting professor at Boston University.