Lincoln was promoted to colonel on September 13, 1944. During World War II, Lincoln took part in the seven conferences between the heads of state and the combined chiefs of staff (Washington, the first and Second Quebec Conferences, Cairo, Tehran, Malta, and Yalta). He was also a member of the Joint Staff Planning and the Army Forces Western Pacific, headquartered in Manila. During the final months of the war, Lincoln served as the chief of transportation in the Pacific Theatre.