3 Group had almost completely re-equipped with the Wellington by 4 September 1939 to carry out the second bombing operation of the war which was against German warships off Brunsbüttel. In 1940 the first of the new four-engined bombers, the Short Stirling, came into service with the Group, being followed in 1942 by the Avro Lancaster. On 3rd/4th November 1943, No. 3 Group played a leading part in the first bombing attack in which heavy bombers made use of the radar bombing aid known as G-H. The target was Düsseldorf; bombs were dropped "blind" and good results were obtained. In July and August 1944, aircraft of this Group equipped with G-H maintained an all-weather attack against flying-bomb sites. Through the D-Day build-up, the liberation of France and conquest of Germany, formations of No. 3 Group attacked railway junctions, marshalling yards, troop concentrations, etc.

During the week ending 25th March 1945, Bomber Command made numerous attacks to prepare for the crossing of the Rhine.