With Alabama's vote to leave the Union, at the age of 37 Morgan enlisted as a private in the Cahaba Rifles, which volunteered its services in the Confederate Army and was assigned to the 5th Alabama Infantry. He first saw action at the First Battle of Manassas in the summer of 1861. Morgan rose to major and then lieutenant colonel, serving under Col. Robert E. Rodes, a future Confederate general. Morgan resigned in 1862 and returned to Alabama, where in August he recruited a new regiment, the 51st Alabama Partisan Rangers, becoming its colonel. He led it at the Battle of Murfreesborough, operating in cooperation with the cavalry of Nathan Bedford Forrest.