In 1931 Hellmayr went back to Vienna. After the Nazi takeover of Austria in 1938, he was arrested and briefly jailed for reasons that are not fully known but probably related to his unsympathic views toward the Nazi Party (Hellmayr did not make political statements in public, but his interest – as an amateur historian – in the French Revolution shows that he was more than casually interested in such topics). After his release he emigrated with his wife to Switzerland. Following a long period of declining health he died in 1944 in Orselina, near Locarno.