He was made captain of in March 1805. In July 1805 he recommissioned the 22-gun for service in the Mediterranean, and in October 1806 took command of the 36-gun . Elliot commanded her for the next six years, and sailed for the East Indies and China on 15 February 1807. On 8 October 1808 he chased down and captured the 18-gun French corvette "Iéna" while in the Bay of Bengal, and on 15 July 1809 boats from "Modeste" and cut out the 8-gun "Tuijneelar" in the Sunda Straits. Elliot then took part in the operations to capture Java between August and September 1811. He took command of the 38-gun in 1813 and was involved in the suppression of Borneo pirates in June. His actions during these campaigns brought the attention of his superiors, as did his assistance to Colonel McGregor in restoring the Sultan of Palembang. The end of the Napoleonic Wars left him without any commands, though he was able to secure a posting to command HMS "Victory", then serving as the guardship at Portsmouth from 1 May 1827 until 24 January 1832. His service during this period earned Elliot the praise of the Duke of Clarence, the future King William IV.