Bainbridge commanded merchant vessels from 1793 to 1798, when he became an officer in the newly organized U.S. Navy. He served in the war with the Barbary States (1801–05) and was in command of the frigate Philadelphia when it was captured by the Tripolitans (1803). Imprisoned for a time, he returned to the merchant marine upon his release (1805). At the outbreak of the War of 1812 he was again commissioned in the U.S. Navy and was given command of the frigate Constitution. His capture of the Java off the Brazilian coast was one of the notable American naval victories of the war and, according to some, helped earn for his ship the sobriquet “Old Ironsides.”