Transferred to Lake Ontario, Elliott served under Commodore Isaac Chauncey as captain on board the flagship the , and took part in the Battle of York on 27 April 1813 and the Battle of Fort George on 27 May. He was promoted to master commandant in July and reassigned to the Lake Erie squadron, to serve as Commodore Perry's second-in-command. He felt Perry had insufficient combat experience, and was particularly critical of Perry's choice of Presque Isle for his shipyard.