After the "seizure of power" by the NSDAP Auer initially went underground and fled to Innsbruck. A short time later, however, he returned to Munich. On 9 May 1933, he was severely abused by the National Socialists in the Munich City Council and imprisoned in the prison Stadelheim. After his release, Auer was banned from visiting Munich and subsequently forced to change his whereabouts and employment. In connection with the assassination attempt of Hitler on 20 July 1944 Auer, now seriously ill, was again arrested, imprisoned in the Dachau concentration camp and probably relocated to Giengen an der Brenz, Württemberg with an ambulance because of the advancing Allied troops, where he died 20 March 1945.