Mayer was arrested again 3 November 1939 and sent to Sachsenhausen concentration camp under the "Kanzelparagraphen", a series of 19th-century laws that forbade the clergy to make political statements. He was released from there on the condition of a broad ban on preaching. The sixty-three-year old priest developed heart problems, From late 1944, he was interned in Ettal Monastery, mainly because the Nazis were afraid that he would die in the concentration camp, and thus become a martyr. He remained there until liberated by the US forces in May 1945.