[1] He worked as a mathematical theoretician and cryptanalyst for the civilian Pers Z S, the cipher bureau of the Foreign Office (German: Auswärtiges Amt), from the spring of 1941 to the end of World War II.

On 1 April 1941 he took a leave of absence to join Pers Z S, the Foreign Office civilian cipher bureau, working as a mathematician.

[1] On 19 March 1943 he presented the application to the Faculty of Philosophy and Natural Sciences, with the publication Axiomatisierung der Fregeschen Aussagenkalküle (English: Axiomatisation of Frege's Propositional Calculus), to be admitted to his Habilitation.

On the basis of the positive opinions of Heinrich Scholz and Adolf Kratzer, the degree of Doctor rerum naturalium habilitatus was awarded to him by certificate of 22 May 1943.

On 18 August 1943 he was appointed lecturer with the authorisation to teach "Mathematical Logic and Fundamental Research", all the while still being employed in Berlin as a "scientific assistant worker" at Pers Z S.[1] Karl Schröter remained at the University of Münster from 31 December 1943 until his contract was up on 31 April 1945, when he was taken prisoner by the Counterintelligence Corps (CIC).