Initially close to the Girondists, Lindet was very hostile to King Louis XVI, provided a Rapport sur les crimes imputés à Louis Capet (December 20, 1792) – a report of the king's alleged crimes – and voted for the king's execution without appeal.
He was instrumental in the establishment of the Revolutionary Tribunal, and contributed to the downfall of the Girondists before the start of the (after a conflict over the Tribunal's radical character). His proposal for the Tribunal had passed with support from Georges Danton, despite the opposition of Pierre Victurnien Vergniaud.
Lindet wrote his accusation as a chronological retelling of the treasonous acts of the King, beginning in May 1789 and spanning until August 10, 1792. Beginning with the eve of the calling of the Estates-General, Lindet argued that Louis XVI intended to use the representatives to raise money for the bankrupt crown, and then send them on their way with few reforms. When this did not prove effective, Louis XVI resorted to the use of military force, which catalyzed the storming of the Bastille, and the movement of the King to Paris. From this point, he focused on the counter-revolutionary actions of the King as showcased by the discovery of the Iron Cupboard, proving that the king was duplicitous. By the summer of 1792, Lindet argued that Louis XVI had realized his counter-revolutionary efforts had proved futile, and he would have to take military action. He provoked the insurrection of August 10 with the gathering of troops at the Tuileries, and when he saw his imminent defeat, the Swiss were left to die for an undeserving king. Lindet would be known to have a strong opinion in this matter because during the Insurrection, he actually worked to help a Swiss guard escape. In his accusation against the king, Lindet focused strongly on his duplicity and betrayal against the actions of the French Revolution. His acte enonciatif characterized the views of the Montagnards, and also violated the Criminal Code of 1791. Another inconsistency in the trial of Louis XVI was that the argument presented against him by Lindet disregarded any account of the Revolutionary violence against the King, thus presenting his accusation as a series of inexcusable crimes against the Revolution.
Very concerned by the question of food supplies, he showed his administrative talent in coping with the issue. Lindet was the department head, or the "examiner" of the National Food Commission. The National Food Commission was mainly in charge of economic measures and more specifically was responsible for the provision of subsistence, clothing, and transportation. This body consisted of over 500 members at the height of the Reign of Terror, and would often send these members out for tasks and the gathering of intelligence. For one of these missions, Lindet was sent to the districts of Rhône, Eure, Calvados and Finistère, for the purpose of suppressing revolts. He was successful and was able to enact a conciliatory policy. The National Food Commission also functioned to supervise agricultural and industrial production, was given control of the labor force for war effort, put in charge of controlling trade, and most importantly, the enforcement of the Law of Maximum.
Without being formally opposed to Maximilien Robespierre, he did not support him, and he was, with Philippe Rühl, one of the only two members of the Committee who did not sign the order for the execution of Danton and his party. When asked to do so, he had replied to Louis de Saint-Just: "I am here to protect citizens, and not to murder patriots".
The French Directory offered Lindet the opportunity to become its spy in Basel, but he turned down the mission. After taking part in the conspiracy of Gracchus Babeuf (1796), he faced trial and was acquitted, and then was elected to the Council of Five Hundred (by Eure and Seine), but was not allowed to occupy his seat. However, he served as Minister of Finance from June 18 to November 9, 1799.
In 1816 he was proscribed by the Bourbon Restoration government as a regicide - avoiding a harsher penalty by not having recognized Napoleon during the Hundred Days. Lindet returned to France some time before his death in Paris.