Following the annexation of Austria into Nazi Germany in 1938, Weixlgärtner was forced to quit his position. His wife, Pepi, had Jewish ancestry, which the Nazi regime would not tolerate, and furthermore, he refused to hand over the keys of the Treasury to the SS. In April 1945, at the very end of World War II, the Nazis burnt down his house and he lost all his belongings, including his large library of art history literature, his private collections, and an academic manuscript ready for printing together with the rest of his property; according to his obituary, "he was not able to save even his everyday clothes".