After being re-equipped with the Short Stirling in November 1941, the squadron took part in the first 1,000 bomber raid. The squadron also formed No. 149 Squadron Conversion flight on 21 January 1942 to train new Stirling crews and on 7 October this was formed into 1657 Heavy Conversion Unit (HCU) together with 7, 101 and 218 Squadron Conversion Flights. In August 1944, the Stirlings gave way to Avro Lancasters, which served the squadron until 1949. At the end of the war no. 149 squadron participated in Operation Manna, to drop food to the starved Dutch population still under German occupation, and Operation Exodus, to return former prisoners of war back to the UK.