When the Civil War began, Maury was the Assistant Adjutant General in the New Mexico Territory, based in Santa Fe. Hearing the news of the firing on Fort Sumter, he resigned from the United States Army and travelled back to Virginia. He entered the Confederate Army as a colonel, serving as an Adjutant General, then was Chief of Staff under General Earl Van Dorn. Following the Battle of Pea Ridge, he was promoted to the rank of brigadier general and assigned to field command. Maury led a division at the Second Battle of Corinth, and was appointed major general in November 1862. He participated in army operations around Vicksburg, Mississippi, and in the defense of Mobile, Alabama. In the latter military campaign, Maury commanded the Department of the Gulf.