During his career as a lawyer and politician, serving in both houses in his native Georgia and in the U.S. Senate, Robert A. Toombs gradually became a secessionist. After attending the state's secession convention, he was named to the Provisional Confederate Congress where he served on the Committee on Finance. An aspirant for the presidency, he instead became the first secretary of state on February 21, 1861. Bored, he stepped down in July and, capitalizing upon his experience as a captain of volunteers during the Creek War, entered the military service.

His assignments included: brigadier general, CSA (July 19, 1861); commanding brigade, 2nd Corps, Army of the Potomac (summer-October 22, 1861); commanding brigade, G.W. Smith's Division, (in Potomac District until March), Department of Northern Virginia (October 22, 1861 - April 1862); commanding brigade, D.R. Jones' Division, Magruder's Command, same department (April-July 3, 1862); temporarily commanding the division (April 1862); and commanding brigade, Jones' Division, lst Corps, Army of Northern Virginia (July and August 30-September 17, 1862).

Seeing action in the Seven Days, he was criticized by D. H. Hill for the behavior of his brigade at Malvern Hill. His demand for satisfaction went unanswered. Still retaining a seat in congress, he was absent for part of the summer but rejoined his command at 2nd Bull Run. At Antietam his brigade performed creditably and he suffered a hand wound. At about the time that congress adjourned he submitted his resignation, which took effect on March 4, 1863. He was disgruntled about being passed over for promotion.

He lost a race for the Senate but was named adjutant and inspector general for the Georgia Militia in the Atlanta Campaign. Fleeing the country to avoid arrest at the war's close, he returned and resumed his law practice. Late in life he suffered from blindness and alcoholism.