On April 11, 1793 he was appointed as commander of the Army of the Moselle and, in the following August, of the Army of the North. He was a protagonist of the French victory at the Battle of Hondschoote against the British army under the Duke of York.
Despite the French victory, Houchard was accused to have not profited of it, and was arrested at Lille on September 24, 1793. When accused of cowardice by the Revolutionary Tribunal, Houchard replied by taking of his clothes and showing his many battlewounds. However, the tribunal found him guilty and Houchard was guillotined in Paris on November 17, 1793 (26 Brumaire, Year II).