On May 22, 1861, Jordan resigned from the U.S. Army and was commissioned as a captain in the fledgling Confederate army. Promotion came rapidly, and by June 1861, he had become a lieutenant colonel and a staff officer, seeing duty at the First Battle of Manassas as a full colonel and chief of staff under P.G.T. Beauregard. He also was the army's adjutant general and accompanied President Jefferson Davis on a post-battle tour of the field.
Jordan subsequently accompanied Beauregard to the Western Theater to Kentucky. During the advance from Corinth, Mississippi, into Tennessee, he rendered valuable service in preparing the men for the Battle of Shiloh, where he was conspicuous in efficiently managing the flow of orders to and from the various corps commanders and their respective staffs.
For his actions at Shiloh, he was promoted to brigadier general on April 14, 1862, and served as chief of staff for General Braxton Bragg during his Kentucky Campaign. When Beauregard was reassigned to the defense of Charleston, South Carolina, Jordan accompanied his long-time friend and mentor as chief of staff for that department. In May 1864, he was assigned to the command of the Third Military District of South Carolina.