After World War II had ended in Europe the squadron operated in the transport role until disbandment in December 1945.

104 Squadron, which was equipped with the Vickers Wellington medium bomber, and 158 sqn used these on night raids to Germany and occupied France.

By 7 May 1945 the Second World War in Europe had finished and the squadron was transferred to RAF Transport Command, re-equipping with the Short Stirling Mk.V.

LV907, coded NP-F and nicknamed "Friday the 13th", completed 128 operational missions and was scrapped after being displayed on Oxford Street in London.

On 11 November 1945 a Stirling C.5 operated by the squadron was departing for the United Kingdom when it crashed on take off from RAF Castel Benito in Libya after the wing caught fire; 21 soldiers and five crew were killed, one person survived.