After the Nazi seizure of power in 1933, his youth work had to cope with increasing repressions by the government authorities and his activities were monitored by the Gestapo.

According to the 2007 documentary Laughing with Hitler, Müller was arrested after repeating a political joke about a wounded soldier on his deathbed, who asked to see the people for whom he was laying down his life.

Müller was interrogated and temporarily taken into custody on 6 September 1943 under charges of comparing Hitler and Göring with the two criminals crucified alongside Jesus Christ.

Although Müller was temporarily released, local Nazi officials re-arrested him on 15 May 1944 and he was deported to the Moabit remand prison in Berlin.

[1] Since the end of World War II, each year on the anniversary of Müller's death, a bell is tolled at his former parish church in the village of Groß Düngen.