Following the war, Augur went on to command several military departments: the Department of the Platte from January 15, 1867, to November 13, 1871; the Department of Texas from November, 1871, to March, 1875; the Department of the Gulf from 1875 to July 1, 1878; the Department of the South from July 1, 1878, to December 26, 1880; and then he returned to the Department of Texas where he commanded for approximately another three years between January 2, 1881, and October 31, 1883. He headed up the Military Division of the Missouri from 1883–85. He also played a major role in negotiating the Treaty of Medicine Lodge in 1867 and the Treaty of Fort Laramie in 1868. A fort in the Wyoming Territory was briefly named Fort Augur in his honor. In 1885, he retired from the Army with the rank of Brigadier General.