Siemens was a senior captain upon the outbreak of World War II and was promoted to flag rank in January 1940. A year later, he was selected to serve under Günther Lütjens as deputy fleet commander of the German Navy. The position did not entail at-sea command, but was an administrative posting overseeing the type commanders within the organization of the "Kriegsmarine". After Lütjens was killed onboard the battleship "Bismarck", Siemens continued his post briefly under Otto Schniewind before the position was disbanded in June 1941.