Reinstated in 1801, Villaret took command of the naval component of the Saint-Domingue expedition, and was appointed captain general of Martinique and Sainte-Lucie alongside the colonial prefect, Charles-Henri Bertin. He served in this capacity until the British captured Martinique in 1809. Returned to France, Villaret fell in disfavour for his perceived weak defence during the invasion. After two years, Napoléon pardoned him and appointed him governor of Venice. Villaret died there of edema on 24 July 1812.