[2][3] Eaton entered the American Civil War as a chaplain of the 27th Ohio Volunteer Infantry on August 15, 1861.

[4] In November 1862, after Lincoln's preliminary Emancipation Proclamation, Major General Ulysses S. Grant appointed him superintendent of freedmen and was later given supervision of all military posts from Cairo to Natchez and Fort Smith.

In November 1863, Grant appointed him as the Superintendent of Negro Affairs for the Department of the Tennessee; there Eaton supervised the establishment of 74 schools.

[3] Eaton wrote a history of Thetford Academy, "Mormons of Today", "The Freedmen in the War", "Schools of Tennessee" and several reports, addresses and magazine articles.

[3] After several years of failing health, he took ill on February 8, 1906, and died one day later in his apartment in the Concord Flats in Washington, D.C.[4] He was buried in Arlington National Cemetery.