In 1799 and early 1800, she was part of Commodore Barry's squadron in the West Indies. Lieutenant Edward Preble commanded Pickering from January through June 1799, when he was promoted to captain and took command of the frigate Essex.
On 21 April, 1799 she exchanged fire with Fort Dup Vieux and Fort Royall, Guadeloupe.[2] On 29 April, 1799 she and USS George Washington recaptured American brig "Fair American" captured by 3 French letters of marque the previous day.[3] On 1 May, 1799 she, and USS George Washington recaptured American brig "Francis", captured by a French privateer. "Francis" was Captained by Joshua Preble, Lieutenant Edward Preble's brother.[4] Pickering was permanently transferred to the Navy on 20 May and re-designated USS Pickering. She arrived at New York 12-13 June, 1799 from her deployment to the Caribbean.[5] Master Commandant Benjamin Hillar,[6] U.S. Navy, assumed command in June, and continued command of the ship for its final years. Under Hillar's command Pickering fought a notable engagement with the French privateer L'Egypte Conquise on 18 October 1799. The Frenchman was well fitted out and manned and should have been able to capture Pickering. While the French ship carried fourteen 9-pounders, four 6-pounders, and crew of 250, the American cutter had only fourteen 4-pounders and seventy men. After a nine-hour battle, however, the French ship was forced to surrender. Pickering continued to cruise in the West Indies, and before her return to the United States had captured four French privateers, including Voltigeuse, Atalanta, L'Active, and Fly, and recaptured the American merchant ship Portland.
Pickering departed from Boston on 10 June 1800. Ordered to join Commodore Thomas Truxton's squadron on the Guadeloupe Station in the West Indies, she sailed from New Castle, Delaware on 20 August, and was never heard from again. She is presumed to have been lost with all hands in a gale in September, but this was never proven. This storm is also thought to have sunk USS Insurgent, which likewise vanished without a trace. The exact cause of the cutter's disappearance remains a mystery.
