When Prof. Wintgen became professor emeritus in 1952, Prof. Gerhard Schmid became principal of the Institute of Physical and Colloid Chemistry.

In 1953 the county of North Rhine-Westfalia took over the university inclusive all institutes from the City of Cologne, which nevertheless paid 50 % of all costs until 1960. Since 1965 the University of Cologne has been a university exclusively financed by the county. 

In 1955, the newly founded Faculty of Mathematics and Natural Sciences, which included the Chemical Institute and the Institute of Physical Chemistry and Colloidal Chemistry, separated from the Faculty of Arts. Founded in 1958 the Institute of Nuclear Chemistry existed independently until its head Prof. Wilfried Herr became professor emeritus, after which it was changed into the Nuclear Chemistry section of the Institute of Biochemistry.

Three years after the death of Prof. Alder, the Chemical Institute was divided into the Institute of Organic Chemistry (director: Prof. Emmanuel Vogel) and the Institute of Inorganic Chemistry (director: Prof. Franz Fehér) in 1961. Founded in 1948 the Institute of Fermentation Sciences was integrated into the new Institute of Biochemistry (director: Prof. Lothar Jaenicke). Until April 1996 the Institute's premises were situated at Bottmühle in Cologne's Südstadt, a couple of kilometres from the university's centre away.

In 1970 the Institute of Physical Chemistry received two chairs (directors: Prof. Dieter Hummel and Prof. Dietrich Woermann). The corresponding expansion was also carried out at the Institute of Organic Chemistry (directors: Prof. Emmanuel Vogel and Prof. Herbert Budzikiewicz). In 1973 the chair for Theoretical Chemistry (director: Prof. Georg Hohlneicher) was added. After Prof. Fehér became professor emeritus, the Institute of Inorganic Chemistry was headed cooperatively by three full professors (directors: Prof. Hans Uwe Schuster, Prof. Marianne Baudler, Prof. Thomas Kruck).

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