While serving on board "Theseus", Atkinson also saw action at Aboukir Bay in 1798 and Acre in 1799, when he was wounded in an explosion that damaged the ship and killed the captain, Ralph Miller. Atkinson was mentioned by Sir Sidney Smith in despatches, later published in the London Gazette, for his bravery in having contributed to the success of the battle and, along with other officers, saving the ship after Captain Miller was killed.