When the Civil War erupted, Loring sided with the South. In a conference in New Mexico, just before he left to defend his homeland, Loring told his officers, "The South is my home, and I am going to throw up my commission and shall join the Southern Army, and each of you can do as you think best." He resigned from the U.S. Army on May 13, 1861. Upon offering his services to the Confederacy, Loring was promptly commissioned a brigadier general and given command of the Army of the Northwest, participating in the Western Virginia Campaign in the fall of 1861. His first assignment was to quickly collect and rally the shattered remnants of Robert S. Garnett's force following its defeat at the Battle of Rich Mountain, and drill them in preparation for the defense of western Virginia against Maj. Gen. George B. McClellan's invasion from Ohio.