War broke out in September 1939 and Möller joined the army. resumed his responsibilities at the , though the association appears to have been pretty inactive till 1945. That year Nirrnheim died a couple of days after his eightieth birthday, and Möller returned from the war to Hamburg, resuming his duties both at the Hamburg History Association and as a senior member of the management team at the city archives. In 1948 he was appointed as director (head) of the in succession to . He took office on 1 January 1948, but was then sent on leave early in February 1948, facing the prospect of dismissal.