At the end of World War II, Aubin was drafted into the Volksturm and fought in the Siege of Breslau. In 1946, Aubin was appointed Professor of Medieval and Modern History at the University of Hamburg. From 1955, he was Honorary Professor of History at the University of Freiburg. After the war, Aubin founded and led a number of scholarly organizations. He was the Editor of Zeitschrift für Ostmitteleuropa-Forschung from 1952 to 1966. Aubin played a leading role in shaping the field of history in West Germany. On his 70th birthday in December 1955, Aubin received the Grand Cross of the Order of Merit of the Federal Republic of Germany. He died in Freiburg 11 March 1969.