The Royal Navy took her into service as the brig HMS "Cesar". Head money for the capture was paid in June 1829. In July 1806 "Polyphemus" was recommissioned. Captain Joseph O. Masefield replaced Redmill in September. In the action of 25 September 1806, a British squadron of six ships of the line that was keeping a close blockade of the port as part of the Atlantic campaign of 1806 intercepted a French squadron comprising five frigates and two corvettes, sailing to the French West Indies with supplies and reinforcements. The British ships, under the command of Commodore Sir Samuel Hood sighted the French convoy shortly after it left Biscay port of Rochefort. The British caught the French convoy after a five-hour pursuit, although they had become separated from one another during the chase. The British captured the French frigates "Infatigable", "Minerve", "Armide", and "Gloire". "Polyphemus" shared in the prize money for these four frigates. Captain John Broughton replaced Masefield in October. In 1807 "Polyphemus", under the command of Captain Peter Heywood, became the flagship of Rear-Admiral Sir George Murray, off South America. In March Murray's squadron carried troops from the Cape of Good Hope to South America in support of a second failed attempt to wrest the River Plate area from the Spanish. A detachment of sailors and marines from "Polyphemus" served on shore in the Advance Brigade during the disastrous (for the British) attack on Buenos Aires. Admiral Murray evacuated Lieutenant Crowley of "Polyphemus", who had been wounded, and his men, aboard the frigate {[ship|French frigate|Néréide|1779|2}}. "Polyphemus" remained in the River Plate area, carrying out surveying and merchant vessel protection duties. Between January and February 1808 "Polyphemus" underwent a refit at Portsmouth. Heywood remained in command until May 1808, when Captain William Pryce Cumby replaced him. Cumby had been lieutenant and then acting commander of at Trafalgar. "Polyphemus" became the flagship of Vice-Admiral Bartholomew Samuel Rowley. In July she sailed for Jamaica, convoying a large fleet of merchantmen, and taking the Vice-Admiral to take up his appointment as chief of the station. Since he resided on shore with his flag in , "Polyphemus" was able to undertake cruises against the enemy.