Clanton and his regiment reached Mexico City following the September 1847 battle and after the occupation there had ended he returned home to Alabama.

After the war, Clanton resumed studying law and in 1850 was admitted to Alabama's bar association, settling in Montgomery.

He first served along the Florida coast until the fall, when he was appointed a captain in the Alabama Cavalry on November 12.

Beginning that September he was given command of the 2nd Brigade in the Confederate Gulf District, holding this post into early 1864.

"[4] Clanton fought during the 1864 Atlanta Campaign, notably in the engagement on July 14 at the Ten Island Ford of the Coosa River against Union Maj. Gen. Lovell H. Rousseau.

In this battle Clanton reportedly "lost his entire staff" and "His bravery made him well known by the generals of the Army of Tennessee."

In January 1865 Clanton was appointed to command the Cavalry Brigade of the District of the Gulf within the same department.

Clanton, aware of the strong Union sentiment in East Tennessee during the Civil War, felt he was entering hostile territory, and became convinced that the railroad company was going to try and assassinate him.

The trial concluded on April 30, and the jury deliberated for just five minutes before voting to acquit Nelson.