From 1793 to 1795, Pérignon held commands in the Army of the Eastern Pyrenees, defeating the Spanish troops at the battle of Escola with "a sombre kind of energy".

He became the French Directory's ambassador to Spain, concluding the Treaty of San Ildefonso against the Kingdom of Great Britain.

Pérignon was a supporter of Napoleon Bonaparte, and was made a senator (1801), Marshal (1804) and count of the French Empire; in 1805, he received the Legion of Honor.

Later moved to the Kingdom of Naples, Pérignon, recently ennobled, became a close acquaintance of the royal couple (King Joachim Murat and Caroline Bonaparte).

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.