Heathcote remained in the West Indies until April 1805, when he took command of the 36-gun and sailed her back to Britain escorting a convoy of 101 ships, afterwards paying her off. He was appointed to command the Isle of Wight Sea Fencibles on 21 March 1807, and received his next sea-going command in February 1808, when he took over the 64-gun . He made two voyages to India, carrying Gore Ouseley and Mirza Abolhassan Khan Ilchi, the ambassadors between Persia and Britain. They would be instrumental in arranging for Heathcote's knighthood in 1819. Heathcote then sailed to the East Indies in July 1810 and served at the capture of Java in 1811. His service here was not without controversy, and on 30 August 1811 he was tried by court-martial for breach of the 27th article of war, for disobeying orders, and for neglect of duty.