However, the Assembly's bar did not disapprove of his conduct.
Chalier later ran for mayor of Lyon in November 1792, but lost to the Royalist opposition.
Soon after, Chalier became the leader of the Jacobins of Lyon, a move which ultimately led to his demise.
Working with other revolutionary clubs and communes in the city, he led the Jacobins to arrest a great number of Royalists during the nights of the 5th and 6 February 1793.
This brought him into direct conflict with the mayor of Lyons, who had the support of the National Guard.
Undeterred, Chalier demanded of the Convention an establishment of a revolutionary tribunal and a revolutionary army stationed in Lyon.
The Convention refused and the anti-revolutionary party took action.
On the 29th and 30 May 1793, the different sections of the Convention rose against him.
The Jacobins were dispossessed of the municipality and Chalier was arrested.
On the 15th of July, he was brought before the criminal tribunal of the Rhône-et-Loire, which condemned him to death.
He was guillotined the next day in Lyon.
Soon after, the revolutionary forces during the "reign of terror" held his memory in high esteem, as a martyr for Liberty.