At the outbreak of the Civil War in 1861, Gates enlisted in the Confederate Army, starting as a captain in the Missouri State Guard under the command of General Sterling Price, and was later promoted to colonel of the 1st Missouri Cavalry Regiment. He commanded his regiment at the Battle of Pea Ridge, Arkansas in March 1862, during the Siege of Corinth, Mississippi, and at the Battles of Iuka, Second Corinth, Champion Hill, Big Black River Bridge and at the Siege of Vicksburg, Mississippi. In 1864, Gates participated in the Atlanta Campaign and the Battle of Allatoona, Georgia, and lost an arm at the Battle of Franklin, Tennessee. During his service, he was wounded five times, captured by Union forces three times, and had four horses shot from underneath him. On April 9, 1865, the same day Confederate General Robert E. Lee surrendered to Union General Ulysses S. Grant, Colonel Gates was engaged in one of the last battles of the Civil War, the Battle of Fort Blakeley in Alabama.