Captain Thomas Baker subsequently took command of "Phoebe" in May 1801. In June 1802 Capt. James Shephard took command. Captain The Hon. Thomas Bladen Capell followed him and recommissioned "Phoebe" in September. She then sailed for the Mediterranean on 28 September. In 1803 "Phoebe" was sailing out of Malta. At some point, perhaps during the summer, her boats participated in a disastrous attack on two French privateers off Civitavecchia. The privateers repulsed the British, who lost eight men killed and wounded. On 1 August, "Phoebe" captured two settées, which a French squadron recaptured. In recapturing the settees, the French squadron involved lost an opportunity to capture "Phoebe", though they did capture the schooner and a transport. On 13 June "Phoebe" and "Amazon" made ready to engage two French frigates anchored under the guns of the north-most fort at Toulon. The fort fired at "Phoebe", but she was out of range. When the French fleet sortied, the British vessels rejoined their squadron, however the French fleet returned to port without engaging. On 24 August 1804 "Phoebe" and captured "Venscab". On 10 November "Phoebe" captured "Cacciatore". Then "Phoebe" and "Hydra" shared the proceeds from the capture between 9 and 15 November of the vessels "Paulina" and "Sesostris". Then, while Nelson was pursuing the French fleet from Toulon to the West Indies, Capel, in "Phoebe", was in charge of a small squadron of five frigates and two bomb vessels with the mission of covering Sicily, Sardinia and the route to Egypt. "Phoebe" joined the blockade of Cadiz later in the summer. The arrival of the additional frigates "Phoebe", , , , and off Cadiz allowed Nelson to detach them to disrupt local shipping supplying provisions for the Franco-Spanish Combined Fleet in Cadiz. In October, the frigate squadron was acting as the eyes of the British fleet. When the Combined Fleet put to sea on 19 October, "Phoebe" was first in line, followed by "Naiad" and the third rate . Capel spotted the Combined Fleet's exit and notified Nelson. As the combined fleet approached the British over the next couple of days, the frigates shadowed it, reporting on its movements.