Politically, Watts adopted a pro-Union stance during the 1850s, but subsequent developments made the depth of his beliefs questionable, for on the eve of the Civil War he played an important role in the secession of Alabama, and was one of the signers of the secession ordinance. Defeated by John Gill Shorter in an 1861 bid for governor, Watts organized the 17th Regiment Alabama Infantry and led it at Pensacola and Corinth, but resigned as its colonel to become the Confederacy's attorney general in President Jefferson Davis' cabinet.