Elworthy joined the air staff responsible for operations at Headquarters No. 2 Group in May 1941, was promoted to the rank of wing commander on a temporary basis on 1 September 1941 and mentioned in despatches on 24 September 1941. He transferred to the air staff responsible for operations at Headquarters RAF Bomber Command in October 1941 and became Group Captain responsible for operations there in May 1942. Promoted to wing commander on a war substantive basis on 9 November 1942, he was mentioned in despatches again on 1 January 1943. He became Station Commander at RAF Waddington in April 1943 and was mentioned in despatches yet again on 14 January 1944. In April 1944 he was made Bomber Command's Representative to Air Chief Marshal Sir Arthur Tedder, who was then serving as Deputy Supreme Allied Commander, Supreme Headquarters Allied Expeditionary Force. He was, in this role, closely involved in the planning for operations to cut German rail communications. He was made Senior Air Staff Officer at No. 5 Group in August 1944: in this role he was closely involved in the sinking of the Tirpitz in November 1944. He was promoted to group captain on a war substantive basis on 22 February 1945.