In 1939 Müller-Hegemann enlisted as a "staff doctor". Between 1940 and 1941 he was posted to what became the Eastern Front, serving as a . He subsequently returned to Berlin where he worked in an . He had retained his connections to the , where during 1944 he delivered a series of lectures on psychotherapy for Schizophrenia patients. It was also in 1944 that he submitted his habilitation dissertation which under normal circumstances would have resulted in the award of a habilitation degree. However, his work triggered a serious and protracted disagreement with the institute director Harald Schultz-Hencke, who himself published a scholarly paper on the same topic at the same time. It is not clear whether it was the disagreement with Schultz-Hencke or the subsequent incarceration of Müller-Hegemann which meant that he only received his habilitation in 1951.