During the War of 1812 Conner served in Hornet during her chase of HMS Belvedere and her actions with HMS Peacock in February 1813 and the March 1815 capture of HMS Penguin, during the latter of which he was wounded. For a time early in the conflict, he was a prisoner of war. He received promotion to Lieutenant in July 1813.
In the decade following war, Lieutenant Conner served in the Pacific, had shore duty at Philadelphia and commanded the schooner Dolphin. Attaining the rank of Commander in March 1825, he was Commanding Officer of the sloops of war Erie and John Adams before receiving promotion to Captain in 1835.
Connor was given the title Commodore, but his official naval rank remained unchanged. The title "commodore" added nothing to his pay or to his permanent rank of captain. Until 1862, six years after Connor's death in 1856, the title commodore would not come to signify a higher grade or an increased salary.
During the Mexican-American War, Commodore Connor commanded the Home Squadron which operated in the Gulf of Mexico in 1846 and 1847 and executed a brilliant amphibious assault against the city of Veracruz, Veracruz.
Leaving seagoing service soon afterwards, Conner subsequently commanded the Philadelphia Navy Yard. Ill health, however, kept him from seeing much other active employment. Commodore Conner died at Philadelphia on 20 March 1856.