The flotilla was re-formed as "6th U-boat Flotilla" in July 1941 under the command of Korvettenkapitän Georg-Wilhelm Schulz with her base in Danzig. During the first months it was a training flotilla, but when it moved to St. Nazaire in February 1942 it became a combat flotilla. It was disbanded in August 1944, when the last boats left the base for Norway.