Mathews was a slaveholder from Kentucky, as evidenced by the baptismal records of the Osage Mission. Before the Civil War, Mathews was involved in driving off settlers from the adjacent Cherokee Neutral Lands and in stirring Southern sympathies among Native Americans living on the frontier. Early in the spring of 1861, Mathews was commissioned a captain in the Confederate Army and given orders to organize a company of soldiers from among sympathetic Native Americans, specifically, the Quapaw. In June 1861, he held a meeting at the house of Larkin McGhee in the nearby Osage village of Chetopa and organized a company of Osages and mixed-blood Cherokees for the Confederate Army. One of his sons, John Mathews, Jr. joined this company. September 8, 1861, Mathews led another company, this one made up of Osages, mixed-blooded Osages and Cherokees, and border ruffians. This second company raided and looted Humboldt, Kansas, capturing no less than a dozen freed slaves. James Lane put a $1000.00 bounty on the head of Mathews, who was soon betrayed by a man who worked at his ranch. The man helped James G. Blunt and the Kansas 6th Volunteer Cavalry (and the Humboldt Home Guard) track down Mathews. He was killed at the house of William Blythe, rented by Lewis Rogers, just south east of Chetopa on the Cherokee Neutral Lands.