During the Civil War, Miller, a middle-aged soldier with no previous military experience, advanced rapidly from the rank of private to colonel in the 1st Minnesota Infantry. In 1862 Miller returned from the South and replaced Brig. Gen. Henry Hastings Sibley as commander of Mankato's Camp Lincoln. There, 303 Dakota men, convicted of participating in the Dakota War of 1862, awaited their fate. Four months later, Miller supervised, by order of President Lincoln, the mass execution of 38 Dakotas condemned for their part in the war.