He was deputy to the chief of staff of the French expeditionary force destined to Corsica and then, in January 1795, appointed to the military command of Marseille.

He was holding this command when the family of General Napoleon Bonaparte, which had fled their native Corsica during the British occupation of the island, took refuge in the city.

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.

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.