Elliott served in the Confederate States Army within South Carolina from the beginning of the Civil War in 1861 until the spring of 1864, advancing from captain to colonel. In order to participate in the bombardment of Fort Sumter, he attached himself to a different unit than his Beaufort Volunteer Artillery company. The Beaufort Artillery company became an infantry company, so Elliott started his official Confederate Army service as a captain in the 11th South Carolina Volunteer Infantry Regiment. He participated in the defense of Port Royal, South Carolina. He was wounded in the leg at an engagement at Fort Beauregard, South Carolina on November 7, 1861. In August 1862, he was appointed Chief of Artillery for the 3rd military district of South Carolina. He also made some raids against Union targets after the Union Army captured the South Carolina coastal islands, including making attacks with torpedoes. On April 9, 1863, his raiders sank the steamer "George Washington". In 1863, he became major and then lieutenant colonel of artillery. For a time in late 1863, he commanded the Confederate force at Fort Sumter, where he received a head wound during the bombardment of Charleston by Union forces on December 11, 1863.