The rise to power of Napoleon, who became Emperor of the French in 1804, blocked Pacthod's promotion for several years, despite his numerous feats of arms. With the outbreak of the Napoleonic Wars, Pacthod took a notable part to the Battle of Halle and Battle of Lübeck in 1806, was wounded at the Battle of Mohrungen and fought at the Battle of Friedland. Marshal of the Empire Jean-Baptiste Bernadotte, who had been his Corps commander throughout the 1806–07 War of the Fourth Coalition, proposed Pacthod's promotion to General of Division on several occasions, but Napoleon refused. Nevertheless, after fighting brilliantly in several actions in the Peninsular War, especially at Durango (31 October 1808) and Espinosa (10 November 1808), he finally received promotion to the top military rank in the French army, while also being created a Baron of the Empire. In 1809, he fought in the War of the Fifth Coalition, as a part of the "Army of Italy", and took part to the victories of Raab and Wagram. Despite this distinguished service, he was given secondary commands, in the French "Army of Naples", then the "Army of Illyria" and was only able to rejoin the Grande Armée in 1813, for the War of the Sixth Coalition. Following the Battle of Bautzen, Napoleon created him a Count of the Empire (22 May 1813) and less than a week later, Pacthod captured 8,000 Prussians, at the Battle of Hoyerswerda (27 May 1813). During the 1814 campaign for the defense of France, Pacthod was present at virtually every major engagement and was heroic at the Battle of Fère-Champenoise, where he was wounded and taken prisoner. During the Hundred Days Pacthod refused to serve Napoleon and for this he was rewarded by the Bourbon Restoration by being named General Inspector for Infantry, a prestigious position, which was to be the last of his active service.