In 1862, Cooper led Confederate troops at the battles of Elkhorn Tavern, Newtonia and Honey Springs. He was promoted to brigadier general on May 2, 1862, and was named district commander of the Indian Territory on September 29, 1862. This promotion put him in command of all "... (Confederate) Indian troops in the Trans-Mississippi Department on the borders of Arkansas." Rumors circulated that the Indians were dissatisfied with Cooper. To refute this, letters of support from Indian leaders were sent to Richmond, Virginia, to President Jefferson Davis. Cooper commanded the "Indian Brigade" in Indian Territory during Maj. Gen. Sterling Price's second invasion of Missouri in 1864. In 1865, Cooper was appointed Superintendent of the Bureau of Indian Affairs.