On the permanent organization of the Confederate Government, General Bonham was appointed by President Davis a Brigadier General in the Army of the Confederate States.  His brigade consisted of four South Carolina regiments, commanded respectively by Colonels Kershaw, Williams, Cash, and Bacon, and General Bonham used to love to say that no finer body of men were ever assembled together in one command.  With this brigade he went to Virginia, and they were the first troops other than Virginia troops that landed in Richmond for its defense.  With them he took part in the operations around Fairfax, Vienna, Centerville, and the first battle of Manassas.

Afterwards, in consequence of a disagreement with the Department of War, he resigned from the army.  Soon thereafter he was elected to the Confederate Congress, in which body he served until he was elected Governor of this State in December, 1862.  It was a trying time to fill that office, and President Davis, in letters, bears witness to the fact that no one of the Governors of the South gave him more efficient aid and support than did Governor Bonham.  At the expiration of his term of office, in January, 1865, he was appointed to the command of a brigade of cavalry, and at once set to work to organize it, but the surrender of Johnston’s army put an end to the war.

Returning from the war broken in fortune, as were all of his people, he remained for a year or more on his plantation on Saluda River, in Edgefield County.  He then moved to Edgefield Court House, again to take up his practice, so often interrupted by calls to arms.  He was elected to the Legislature in 1866, just preceding Reconstruction, but with the coming of that political era he, in common with all the white men of the State, was debarred from further participation in public affairs.  In the movement known as the Tax-payers Convention, which had for its object the relief of the people from Republican oppression and corruption, he took part as one of the delegates sent by this convention to Washington to lay before President Grant the condition of the people of the “Prostrate State.”  He took an active interest and part in the political revolution of 1876 and warmly advocated what was known as “the straightout policy” and the nomination of Wade Hampton as Governor.

In 1878 Governor Simpson appointed him the first Railroad Commissioner under the Act just passed, and subsequently when the number of the Commissioners was increased to three, he was elected Chairman of the Commission, in which position he continued until his death, on the 27th day of August, 1890.  He died suddenly from the rupture of a blood vessel while on a visit to Haywood White Sulphur Springs, N.C.

General Bonham married on November 13th, 1845, Ann Patience, a daughter of Nathan L. Griffin, Esq., a prominent lawyer of Edgefield.  She survived him four years, and of their union there are living eight children.