As a Whig, Morgan was opposed to secession until 1861, when he joined the Democratic Party. During the American Civil War, Morgan served in the Confederate States Army. He was the founder of the 36th Tennessee Infantry Regiment in Chattanooga, Tennessee in 1861, and served as its Colonel until 1863. He was stationed in Cumberland Gap and fought in Tennessee, Georgia and Kentucky. He took part in the Battle of Murfreesboro and the Battle of Chickamauga. From 1863 to 1864, he was Adjutant-General to Lieutenant-General Leonidas Polk, up until Polk's death. He then served in the Confederate States War Department until 1865, when he was paroled in Atlanta, Georgia.