Stewart was promoted to major following a mission to Ludwigshafen, Germany, on January 7, 1944. He was awarded the Distinguished Flying Cross for actions as deputy commander of the 2d Bombardment Wing, and the French Croix de Guerre with palm and the Air Medal with three oak leaf clusters. Stewart was promoted to full colonel on March 29, 1945, becoming one of the few Americans to ever rise from private to colonel in only four years. At the beginning of June 1945, Stewart was the presiding officer of the court martial of a pilot and navigator who accidentally bombed Zurich, Switzerland.