During the period of denazification following the war, Nazi party members and others who were more than nominal participants in Nazi activities were barred from public posts. Those applying for academic positions had to certify their acceptability.
Klemm was the lead author for the preparation and publication of the six inorganic chemistry volumes of the FIAT review of German science, 1939-1946 (1948-1949). FIAT volumes were compiled by leading German scientists in cooperation with the Military Government for Germany, involving Field Information Agencies Technical from the British, French, and U.S. zones, to report on the scientific work done in Germany during the war years.
From 23 May 1947 to 1951, Klemm led the Inorganic Chemical Institute at University of Kiel (Christian-Albrechts-Universität zu Kiel).  The Institute of Inorganic Chemistry at the University of Kiel has a collection of correspondence and other papers dating from 1947 through the 1960s, relating to Wilhelm Klemm and his successor, Robert Juza.
Klemm's first wife, Lisabeth Klemm (née Herrmann, born 9 October 1895, Eberswalde) died of cancer on 15 October 1948 in Kiel.
In 1949, Klemm married Lina Arndt, a dentist who had been a friend of his first wife.