Mayer spoke out against anti-Catholic baiting campaigns and fought against Nazi church policy. Since he believed that a Catholic could not be a National Socialist, conflict inevitably arose between him and the Nazis. He preached that "Man must obey God more than men". His protests against the Nazis landed him several times in Landsberg prison. Mayer resolutely spoke out against the Nazi régime's evil in his lectures and sermons. On 5 June 1937, he was arrested and found himself in "protective custody" in Stadelheim Prison for six weeks. When he became the target of defamatory attacks on the part of the Nazis, his Jesuit superiors allowed him to return to the pulpit to defend himself against slanders that the Nazis made during his silence. He was re-arrested and served a sentence of five months.