Although he returned to the sea, he was profoundly changed by this spiritual experience, and led an austere, celibate life.

During the Nine Years' War, he was in command of the 54-gun Diamant as part of Châteaurenault's fleet which landed French troops in Ireland, and fought in the Battle of Bantry Bay on 11 May 1689; on 1 November he was promoted to squadron leader.

During the Battle of Beachy Head in July 1690, he commanded a division of the van under Tourville, destroying several Dutch ships.

On board the Vainqueur, Coëtlogon, commanding a squadron with four other ships - the Monarque, Éole, Orgueilleux and Couronne - intercepted a Dutch convoy and defeated its five escorting Dutch warships - the Muiderberg (which was sunk), Rozendaal, Rotterdam, Beschermer, and Gaasterland.

Several ships were named after Coëtlogon, especially a frigate which was active during the Boshin war (1868–1869) in Japan, and later an armoured cruiser.