During the American Civil War of 1861-1865, he was a member of the Confederate Congress and chairman of its Ways and Means Committee. In 1862, he proposed a national income tax of 20%, including a schedule of exemptions. His tax bill went nowhere; but in April 1863, the Confederate Congress passed another act calling for a tax "in kind," payable with goods and agricultural produce rather than money, and based not on property but on agricultural produce and income it generated. In July 1862, while visiting with his family at Ashland Plantation during a recess of the legislature, Kenner narrowly avoided capture by the Union Army, making his escape after being warned by one of his slaves of the advance of Union troops. By this time he had become convinced that the emancipation of slaves was the only way to gain independence for the Confederacy. In 1864, he was sent by Jefferson Davis as special commissioner to England and France to secure the recognition of the Confederate States. Davis, through Kenner, offered the emancipation of the Confederate slaves in exchange for diplomatic recognition of the Confederacy by Britain and France. Following the capture of New Orleans in 1862, much of his property was confiscated and his slaves were freed.