As commander of the frigate USS Chesapeake, he was involved in the Chesapeake–Leopard affair in 1807 which led to the surrender of his ship to the British and resulted in him being court-martialed for his actions during the incident.

Two years later, he was promoted to captain and commanded the sloop-of-war Warren during the final months of the Quasi-War with France.

[2][3] In a letter dated 13 August, 1802 he was ordered to take command of USS New York at the Washington Navy Yard.

[3] Barron obtained the rank of commodore on April 22 and was assigned command of USS Chesapeake the following year.

Chesapeake was berthed at Norfolk and was outfitted for her upcoming mission in great haste with a green crew and equipment that was below standards.

In January 1808, a court-martial was held, and Barron was convicted of not preparing his ship in advance for possible action, and was suspended for five years without pay.

[7] After being away for six years, Barron finally returned from Copenhagen seeking reinstatement, but he remained controversial and was criticized by some of his fellow officers.

Lying wounded, Commodore Barron proclaimed that the duel was carried out properly and honorably and told Decatur that he forgave him from the bottom of his heart.

His personal papers, which primarily relate to the Chesapeake–Leopard affair, can be found in the Special Collections Research Center at the College of William & Mary.