Aylmer transferred again, this time to the command of the second-rate HMS "Royal Katherine" in Spring 1690 and was present at the French victory at Battle of Beachy Head in July 1690. He transferred to the command of the third-rate HMS "Monck" in the North Sea in Summer 1691 and then took command of the first-rate HMS "London" in Spring 1692. As Second Captain to Admiral Edward Russell, he saw action again at the tactically indecisive Battle of Barfleur in May 1692. As a captain, Aylmer was quite deferential to his Spanish partners during the War. Samuel Pepys believed that Aylmer should have been hanged for his habit of dipping his colours to Spanish Admirals.