Elected to the NationalConvention, he sat in the centre, le Marais, voting in the trial of Louis XVI for his detention until deportation should be judged expedient for the state. He was then representative on mission to Lyon, charged with investigating frauds in connection with the supplies of the Army of the Alps. Although he had been close to several Girondists, Boissy d'Anglas escaped arrest after François Hanriot's insurrection of 2 June 1793, and he was one of several centrist deputies who supported Maximilien Robespierre during the early stages of the Reign of Terror. However, he was gained over by the members of The Mountain hostile to Robespierre, and his support, along with that of some other leaders of the Marais, made possible the Thermidorian Reaction. Boissy d'Anglas was then elected a member of the Committee of Public Safety, and charged with the superintendence of the provisioning of Paris. He presented the report supporting the decree of 3 Ventôse of the year III, which established freedom of religion. In the critical days of Germinal and of Prairial of the year III, he was noted for his courage. On 12 Germinal, the day of insurrection of 12 Germinal year III, he was in the tribune, reading a report on the food supplies, when the hall of the Convention was invaded; when they withdrew he quietly continued where he had been interrupted. During Insurrection of 1 Prairial, he was presiding over the Convention, and remained in his post despite insults and menaces of the insurgents. When the head of the deputy, Jean-Bertrand Féraud, was presented to him on the end of a pike, he saluted it impassively.
Under the Directory
He was protractor of the committee which drew up the Constitution of the Year III which established the French Directory; his report shows apprehension of a return of the Reign of Terror, and presents reactionary measures as precautions against the re-establishment of "tyranny and anarchy". This report, the proposal that he made to lessen the severity of the revolutionary laws, and the eulogies he received from several Paris sections suspected of Royalism, resulted in his being obliged to justify himself. As a member of the Council of Five Hundred, Boissy d'Anglas became more and more suspected of Royalism himself. He presented a measure in favour of full liberty for the press, which at that time was almost unanimously reactionary, protested against the outlawry of returned émigrés, spoke in favour of the deported priests and attacked the Directory. Accordingly, he was proscribed immediately after the 18 Fructidor coup, and lived in Great Britain until the establishment of the French Consulate.