His sympathies were now with the Gironde, and after the insurrection of the 12th Prairial (31 May 1793) his life was in danger. He returned to Sompuis, and was saved from arrest possibly by the protection of Georges Danton and in some degree by the impression made by his mother's courageous piety on the local commissary of the Convention. In 1797 he was returned by his départment (Marne) to the Council of the Five Hundred, where he allied himself especially with Camille Jordan. He made one great speech in the council in defence of the principles of religious liberty, but the coup d'état of Fructidor (4 September 1797) drove him back into private life.
It was at this period that he developed his legitimist opinions and entered into communication with the comte de Provence (later Louis XVIII of France). He was the ruling spirit in the small committee formed in Paris to help forward a Restoration independent of the comte d'Artois and his party; but with the establishment of the Consulate he saw the prospects of the monarchy were temporarily hopeless, and the members of the committee resigned. From that time until the Restoration Royer-Collard devoted himself exclusively to the study of philosophy. He derived his opposition to the philosophy of Condillac chiefly from the study of Descartes and his followers, and from his early veneration for the fathers of Port-Royal. He was occupied with developing a system to provide a moral and political education consonant with his view of the needs of France. From 1811 to 1814 he lectured at the Sorbonne.
From this time dates his long association with François Guizot. Royer-Collard himself was supervisor of the press under the first restoration. From 1815 onwards he sat as deputy for Marne in the chamber. As president of the commission of public instruction from 1815 to 1820 he checked the pretensions of the clerical party, the immediate cause of his retirement being an attempt to infringe the rights of the university of Paris by awarding diplomas, independent of university examinations, to the teaching fraternity of the Christian Brothers. Royer-Collard's acceptance of the Legitimist principle did not prevent a faithful adhesion to the soèial revolution effected in 1789, and he protested in 1815, in 1820, and again under the monarchy of July against laws of exception.
He was the moving spirit of the "Doctrinaires," as they were called, who met at the house of the comte de Ste Aulaire and in the salon of Madame de Staël's daughter, the duchesse de Broglie. The leaders of the party, beside Royer-Collard, were Guizot, PFH de Serre, Camille Jordan and Charles de Rémusat. In 1820 Royer-Collard was excluded from the council of state by a decree signed by his former ally Serre. In 1827 he was elected for seven constituencies, but remained faithful to his native department. Next year he became president of the chamber, and fought against the reactionary policy which precipitated the Revolution of July. It was Royer-Collard who in March 1830 presented the address of the 221. From that time he took no active part in politics, although he retained his seat in the chamber until 1839. Whilst during the first half of the nineteenth century the word "liberal" was generally synonymous with Voltaireanism and hostility to the Jesuits, certain speeches of Royer-Collard quoted by Barante show that this liberal, especially in his later years, professed a deferential attachment for the Church. "If Christianity", he wrote, "has been a degradation, a corruption, Voltaire in attacking it has been a benefactor of the human race; but if the contrary be true, then the passing of Voltaire over the Christian earth has been a great calamity." In a letter to Père de Ravignan he comments upon the institution of the Jesuits as a wonderful creation.
He died at his estate of Chateauvieux in the Berry, south of Blois. He had been a member of the Académie française since 1827. Royer-Collard had married in 1799 M.lle de Forges do Châteauvieux. The two daughters who survived to womanhood received an education of the utmost austerity.
Royer-Collard left no considerable writings, but fragments of his philosophical work are included in Jouffroy's translation of the works of Thomas Reid. The standard life of Royer-Collard is by his friend Prosper de Barante, Vie politique de M. Royer Collard, ses discours et ses écrits (2 vols, 1861).