 After the war, Floyd-Jones served in a variety of administrative posts, commanding Newport Barracks in Kentucky from October 1865 to March 1866, and the occupation garrison of Little Rock, Arkansas, from March to August 1866.Following sick leave, he was assigned as Acting Assistant Inspector General and Judge Advocate of the Department of Arkansas from December 1866 to February 1867.He was then in command of Fort Smith, Arkansas until October 1867, and then of Fort Gibson and the District of Indian Territory until January 1868.