In 1796, while Morlot's soldiers were garrisoning Aachen and its district, he was involved in a dispute with a government official and suspended from command. Restored to service, he thereafter held posts in the interior or was inactive for many years. In 1808 when Emperor Napoleon invaded Spain in the Peninsular War, Morlot was given a division of recruits. He led these soldiers at the Battle of Tudela that year and the Second Siege of Zaragoza in 1809, dying of a fever contracted during the siege. His surname is one of the names inscribed under the Arc de Triomphe. He is buried at the cimetière du Père-Lachaise.