Pike's ties to the Indians led to the events that transformed his life. At the outbreak of the Civil War he was named commissioner of Indian affairs for the Confederacy. He succeeded in winning most of the Arkansas tribes over to the Confederacy, and, after being commissioned brigadier general, he organized and armed several Indian regiments. In early March 1862, over his objection that the Indians had agreed to fight only in defense of their territory, Pike's regiments were ordered to take part in a Confederate offensive. On 7 March, during the battle of Pea Ridge, in northwestern Arkansas, the Indians mutilated some Union dead, an infamy that haunted Pike for the rest of his life. On 15 March 1862, the Boston Evening Transcript
doubted that "a more venomous reptile than Albert Pike ever crawled the face of the earth."
Pike, meanwhile, became embroiled in controversy closer to home. On 31 July 1862, confronted with an order to release his units to another command, he published an open letter to the Indians in which he announced his resignation and indicted the Confederacy for neglecting its treaty obligations. Jefferson Davis accused Pike of treason. In November Pike's commanding officer, Major General Thomas C. Hindman, sent 200 soldiers to arrest him, but as the Confederate position in the West collapsed, Pike was released.