In the early post-war years the institute was supported by the Berlin City Council. However, scientific work was only barely possible. Robert Havemann, who had held a scholarship at the institute in 1932 and 1933, was appointed head of the institute by the City Council. In Hitler Germany time Havemann had played a key role in the antifascist group "European Union". He was caught by the Nazis, and in 1943 sentenced to death. The execution was postponed, and he was luckily freed from prison by the Soviet troops in 1945. I. N. Stranski, K. Molière and K. Ueberreiter resumed their work at the institute as best as possible considering the external conditions. Hartmut Kallmann, who had worked with Haber for many years before 1933, returned to the institute from his industrial refuge for a short time. In 1948, however, he accepted an offer to become Professor of Physics at the New York University.

The districts within the U.S. occupation zone did not resume responsibility and financing of the institute until June 1947. At that time the institute received a grant for the "German Research Colleges of Berlin-Dahlem". This organization included the institute together with Otto Warburg's Institute for Cell Physiology and a group of several other Kaiser-Wilhelm Institutes. In January 1948 R. Havemann was charged with being an active member of the communist party, and by order of the American authorities he was dismissed as director of the institute, but was still retained as a Department Head. His department, however, was closed in the beginning of 1950, when he was accused of communist propaganda and banned from the institute. He subsequently moved to East Berlin, where he already had held a professorship for physical chemistry at the Humboldt university since 1947.

In the spring of 1948 a department was set up in the institute for Karl Friedrich Bonhoeffer who was at the same time director of the Institute for Physical Chemistry at the Humboldt-University of East-Berlin. In December 1948 he was appointed director of the institute, but in 1949 he accepted the invitation of the newly founded Max-Planck Society to become director of the new Max-Planck Institute for Physical Chemistry in Göttingen. Nevertheless, he continued to lead the institute until March 31, 1951. He brought Ernst Ruska, the inventor of the electron microscope, to the institute as leader of a Department of Electron Microscopy. Ruska was to set up this new department (while still retaining his employment at Siemens) in order to encourage fundamental research and further development in the field of electron microscopy.

In his Department of Physical Chemistry and Electrochemistry, Bonhoeffer attracted young scientists to work in new fields of research. Georg Manecke developed new ion and electron exchange type polymers, and produced the first immobilized enzymes, i. e. enzymes coupled to polymer matrices, which are now of great importance in biotechnology. Klaus J. Vetter built up a successful team in electrochemistry. He developed new methods for the analysis of the kinetics of electrochemical reactions and made an important contribution to the understanding of the resistance of metals to corrosion. In 1961 both Manecke and Vetter moved to the Free University, as Professors of Organic Chemistry and Physical Chemistry, respectively, but they still kept some institute laboratories as External Scientific Fellows of the institute.

Apart from the department of the institute director there was a large department headed by Iwan N. Stranski who held also a position as Professor of Physical Chemistry at the Technical University of Berlin. His department focused on investigations concerning crystal structure, nucleation and crystal growth processes. At a later stage, also studies on properties of zeolites and of catalytic processes in such microporous solids were performed. In 1954 I. N. Stranski became Deputy Director of the institute.

Erwin W. Müller, the inventor of the field electron microscope, had been working as an assistant in Stranski's department since 1947. During this period he developed the field ion microscope which could achieve extremely high resolution of atomic structures. In 1950 E. W. Müller was given his own department in the institute but in 1952 he took up an appointment in the USA. He remained connected with the institute as an External Scientific Fellow until his death in 1977.