Harris initially vehemently opposed secession, including in a large political rally in Rockbridge, but George Deneale took the opposite position, and Harris later lobbied voters to elect delegates who would allow a referendum on secession, which passed nearly unanimously in the county.

He became known for his "frank and manly" acceptance of the war's results, including his charge to the grand jury on May 11, 1867, exhorting members to do their duty "without fear or favor.

"[6] Upon Virginia's adopting a new Constitution which forbad slavery and thus allowed its readmission to the Union in 1869, and restoration of civil rights to Confederate officials, Harris ran for the U.S. House of Representatives at a special election held in July 1869, but lost.

Harris served as chairman of the Virginia Democratic Convention in 1884, and was a commissioner to the 1893 World's Columbian Exposition in Chicago, Illinois.

His papers, including a diary, are held in the special collections division of the James Madison University library.