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.
Napoleon assigned Decrès command of the frigate squadron accompanying Brueys's fleet during their expedition to Egypt. He participated in the disastrous French defeat at the Battle of the Nile aboard the 40-gun frigate Diane and escaped to Malta, where he took control of the 80-gun ship Guillaume Tell. During the years 1799-1800, Decrès relieved Rear Admiral Jacques Bedout of his command.