Following his return to the United States in mid-1942, Wilkes attended the Naval War College, then became Commanding Officer of the new light cruiser , taking her to the Mediterranean Sea to participate in the invasion of Sicily in July 1943. From August 1943 Rear Admiral Wilkes had amphibious force commands in England and France, playing an important role in preparations for the invasion of Normandy in June 1944, and the invasion of Southern France two months later. As the Allied ground offensive moved into Germany, Wilkes was in charge of U.S. Ports and Bases in France, materially assisting the offensive with his management of logistics.