Gilly joined the French Revolutionary Army in August 1792, and the following month he was promoted to lieutenant colonel of his battalion.

He was promoted to chef de brigade in September of 1793 for the numerous military engagements he fought in while serving in the Army of the Eastern Pyrenees he had recently joined.

[3] After being informed in late June of 1815 about Napoleon's defeat at the Battle of Waterloo, Gilly, then stationed in the Midi region, initially defeated a group of Catholic royalists in the towns of Alès and Uzès; he was later forced into hiding in the predominantly Protestant Cévennes by the presence of the Bourbons.

His uncaptured presence in the Cévennes spread fear amongst Catholics, evoking memories of the violent Camisard Revolt.

[4] Following Napoleon's exile to Saint Helena, he fled to the United States of America after the Bourbons forced him out of France.

[1] Shortly after his release from prison in Spain, Gilly married a woman named Thérèse and the two would go on to have four children.