With the secession of Georgia and the start of the Civil War in 1861, Doles enlisted in the Confederate Army along with most of his militia unit and they were incorporated as Company H in the 4th Georgia Volunteer Infantry Regiment. They were mustered into service on April 26, 1861 in Milledgeville and left for Augusta the next day. On May 9, 1861, he was appointed colonel of the regiment and led it during the Peninsula Campaign as a part of the Army of Northern Virginia. He was wounded at the Battle of Malvern Hill.