After the 18 Brumaire he returned to France. In 1801 his name was erased from the list of emigres by Napoleon; in 1803, after the Saint-Domingue expedition he was sent to Antwerp as commissioner-general and maritime prefect to supervise the erection of defence works, and the creation of a fleet. Malouet left the city in 1807. He was peered and entered the council of state for the navy in 1810. Having offended the emperor by his criticism of the campaign in Russia, he was disgraced and left office in 1812. At the Restoration, Louis XVIII made him Minister of the Navy, but Malouet died the same year. His memoires were published in 1868.