In October 1793, Decrès was sent as a messenger to request assistance for the Isle de France (now Mauritius). He was arrested on his arrival in Lorient, on 10 April 1794, for being a member of the nobility. He was restored to his rank of capitaine de vaisseau in June 1795, and promoted to command of the 80-gun ship "Formidable" in October 1795. While in command of her, he took part, as a division commander, in the failed attempt to invade Ireland in 1796. Promoted to contre-amiral in April 1798, he was in command of a light squadron during the campaign in Egypt, covering the landing on Malta. Napoleon appointed him to command the frigate squadron accompanying Brueys's fleet in the expedition to Egypt, and took part in the disastrous French defeat at the Battle of the Nile on the 40-gun frigate "Diane" and managed to escape to Malta, where he hoisted his flag aboard the 80-gun ship "Guillaume Tell". During the period of 1799 - 1800, Decrès had under his command a rear admiral, Jacques Bedout, whom he saw fit to relieve of his command. Bedout's subsequent resignation was refused and in 1802, Napoleon gave Bedout a five-ship squadron. The flagship was the "Argonaute".