Pérignon subsequently became involved in a smuggling affair and was compromised by a young woman who was a Royalist spy. In 1798 he was recalled and remanded to the Army in Liguria where he was assigned to command the left wing. Wounded and captured by Second Coalition armies at the Battle of Novi, he returned to France in 1800.
He returned to France in 1814 and rallied to the Bourbon Restoration and Louis XVIII - he was stricken off the list of Marshals during the Hundred Days, and voted in favor of the death penalty for Michel Ney. He was raised to marquis de Pérignon, a Peer of France, and awarded the Order of Saint Louis. As Dr. George Ostermann commented, "M. de Perignon died as if the Empire he served well, though reluctantly, had never existed."