In January 1945, the squadron was re-equipped with B-24 Liberator heavy bombers and undertook its first operation two months later out of Cunderdin—refuelling in northern Western Australia at Corunna Downs and Truscott—to bomb targets in the Dutch East Indies. For the rest of the war, No. 25 Squadron was tasked with attacking Japanese shipping and base facilities in the Dutch East Indies. The squadron also assisted in the Allied landings at Brunei Bay in northern Borneo, having re-located to Tarakan in June 1945. In the months following the end of the war, No. 25 Squadron aircraft evacuated liberated prisoners of war to Australia from Morotai and Borneo. The squadron was disbanded in July 1946. Its wartime losses amounted to 25 personnel killed.