He was elected to the National Convention in the same year, voting in favor the capital punishment for King Louis XVI, with the possibility of appeal to the people.
His association with the Girondists nearly involved him in their fall of May–June 1793, despite Lecointe-Puyraveau's extreme Republicanism - he had placed his position in peril after publicly accusing Jean-Paul Marat for having instigated the September Massacres, and even called him "demented", but had not voted in favor of his prosecution.
At the precise moment of the Girondists' proscription, Lecointe-Puyraveau was representative on mission to the Vendée, and, back in Paris during the Reign of Terror, remained an inconspicuous presence in the face of the Committee of Public Safety.
He took part in the Thermidorian Reaction which brought down Maximilien Robespierre, but protested against the establishment of the Directory, and continually pressed for severer measures against the émigrés, and even their relatives who had remained in France.
After six weeks imprisonment in the Château d'If, he returned to Paris, escaping, after the proscription of the regicides (those who had voted for the death of the previous king), to Brussels, where he died a decade later.