In the decade following the War of 1812, Lieutenant Conner had shore duty at Philadelphia and commanded the schooner USS Dolphin. Attaining the rank of Commander in March 1825, he was commanding officer of the sloops of war USS Erie and USS John Adams before receiving promotion to captain in 1835.
In 1841, he became a naval commissioner and was later Chief of Bureau of Construction, Equipment & Repair. Late in 1843, he took command of the West Indian and Home squadrons.
He led U.S. naval forces in the Gulf of Mexico during the first months of the Mexican War 1846-1847. During this time, he was responsible for amphibious operations against several coastal towns and for the successful landing of the U.S. Army at Vera Cruz in March 1847.
Leaving seagoing service soon afterwards, Conner subsequently commanded the Philadelphia Navy Yard. However, ill health kept him from seeing much other active employment. Commodore Conner died in Philadelphia on 20 March 1856 and is buried at the Laurel Hill Cemetery.
Two destroyers have been named after him.
--Brock-Perry
