Scott-Bowden saw early service in Norway in 1940, before joining the 53rd (Welsh) Infantry Division as an Adjutant in 1941. During 1942 and 1943 he served as a on liaison duty with Canadian and American forces. In late 1943 Scott-Bowden joined the reconnaissance unit tasked with scouting the beaches for the D Day landings.
At midnight 31 December 1943, with another Royal Engineer, Sergeant Bruce Ogden-Smith, as members of the Combined Operations Pilotage Parties (COPP), during Operation Bell Push Able, he landed on Gold Beach to take samples of the material from the beach.
They found that the sand, in places, was thin and supported by weak peat material. They took samples back to the United Kingdom that allowed planners to cope with the weaker than expected beaches. On D Day both Sgt. Ogden-Smith and Maj. Scott-Bowden assisted in piloting the initial American landings on Omaha Beach. He then went onto command 17 Field Squadron for the remainder of the War.