He was promoted to lieutenant colonel on 8 February 1813, and appointed to command the garrison at Prescott on the St. Lawrence River.
Although Prevost cautioned him on 20 February to remain on the defensive, Macdonell launched an attack two days later using detachments of reinforcements which were passing through Prescott to bolster his militia.
The resulting Battle of Ogdensburg largely cleared the Saint Lawrence for use as a British supply line for the rest of the war.
In October he was ordered to move to reinforce Lieutenant Colonel Charles de Salaberry's troops south of Montreal.
He became increasingly embittered and apparently unbalanced over what he saw as lack of recognition of his services, although he became a Companion of the Order of the Bath in 1817.