In March 1937 Schniewind was removed from his university post and early in 1938 the authorities launched a criminal investigation case into his involvement with the Confessing Church. He was obliged to take an 80% salary cut. Many sources assume or imply that he remained deprived of his professorship till war ended in May 1945, but recent investigation of personnel records retained in the archives at the University of Halle has indicated that Schniewind's professorship was quietly restored in some form later in 1938. There is no report of the criminal case having reached the stage of a prosecution. According to one source, alongside his lecturing activities on behalf of the Confessing Church, he was able to continue "mentoring his students privately". After 1939 he combined his activities at the university with work as a military-hospital chaplain.