Whilst at sea in February 1800, "Swiftsure" was caught in a gale and badly damaged, having to return to Gibraltar for repairs. On returning to service with the squadron, an enemy fleet was seen on 7 April, having sailed from Cadiz bound for Lima. Two frigates and a number of merchantmen were subsequently captured. "Swiftsure" followed up this success on 12 April by capturing a Spanish schooner. She then became Sir Richard Bickerton's flagship during the blockade of Cadiz, before being assigned to the fleet under Lord Keith. Keith's fleet covered the landings at Aboukir on 8 March 1801, where "Swiftsure"′s naval brigade helped to repulse French counter-attacks. Because several of her men were wounded and others sick, Keith removed 80 of "Swiftsure"s best men and then sent her to Malta as a convoy escort.