All of Alfred Scales's Civil War service was with Robert E. Lee's Army of Northern Virginia. Soon after the call for troops from Washington he volunteered as a private in the North Carolina service, but was at once elected captain of his company, H of the 13th North Carolina Infantry Regiment, and was elected to succeed General William Dorsey Pender as colonel on November 14, 1862. He was engaged at Yorktown and the Battle of Williamsburg in the Peninsula Campaign, and in the Seven Days Battles near Richmond. After Malvern Hill, he collapsed from exhaustion and came near to death. His superior, Brig. Gen. Samuel Garland, Jr., said in his report that Scales was "conspicuous for his fine bearing. Seizing the colors of his regiment at a critical moment at Cold Harbor and advancing to the front, he called on the 13th to stand to them, thus restoring confidence and keeping his men in position." It took him until November to recuperate so he missed the battles of both Second Manassas and Antietam, but returned in time for the battles of Fredericksburg and Chancellorsville.