Emory served as a brigade commander in the Army of the Potomac in 1862, and was transferred to the Western Theater. He was promoted to brigadier general of volunteers on March 17, 1862. He later commanded a division in the Port Hudson campaign. He subsequently returned to the East as the commander of the Nineteenth Corps, serving in all the major battles in the Shenandoah Valley Campaign of 1864, especially at the Battle of Cedar Creek, where Emory's actions helped save the Union army from a devastating defeat until Maj. Gen. Philip Sheridan's arrival.