Putting to sea the next day, New York cruised the waters near Guadeloupe on patrol protecting U.S. merchant ships until forced to return to St. Kitts on 31 December by a bad outbreak of fever among her crew.

With the ratification of Pinckney's Treaty with France on 3 February, she was ordered to return home on 23 March and arrived at New York in late April, remaining there until sailing to Washington in mid-May.

[4] The small Moorish kingdoms on the Barbary Coast of North Africa were attacking American ships, killing and imprisoning crewmen and stealing cargo, while demanding high monetary tribute as their price for ending these piratical acts.

En route on 25 April, a powder explosion in the Gunner's Store Room in the cockpit, caused by a candle, set off 444 blank cartridges that killed four men and damaged the ship, the fire taking an hour and a half to extinguish, forcing the squadron to put into Malta from 1–19 May while she effected repairs.

The frigate remained there replenishing and allowing her crew to see the sights of the island until sailing for Gibraltar on 8 July by way of Naples and Málaga and arriving on 14 September.

[8] She sailed for home on 19 October,[9] stopping at Tunis for supplies on 4 November, she returned to Washington Navy Yard on 9 December 1803 and was immediately placed in ordinary.