At the beginning of the civil war, Colquitt was appointed captain in the 6th Georgia Infantry. Eventually rising to colonel, he led his regiment in the Peninsula Campaign. At Seven Pines, he assumed brigade command after Brig. Gen Gabriel Rains was wounded, and led it through the Seven Days Battles. He led his brigade under Stonewall Jackson in the Battle of South Mountain, Battle of Antietam, the Battle of Fredericksburg, and the Battle of Chancellorsville. Colquitt survived Antietam unscathed although nearly every other officer in the brigade was killed or wounded. After the battle, he was immediately promoted to brigadier general, to rank from September 1.