Here he was brilliantly successful, and his career was flourishing when he came under the influence of Jean du Vergier de Hauranne, the spiritual director and leader of the convent of Port-Royal, and was drawn in the direction of Jansenism.

[3] His book, De la fréquente Communion (1643), was an important step in making the aims and ideals of this movement intelligible to the general public.

[5] The Jesuit Nicolas Caussin, former penitentiary to Louis XIII, was charged by his order of writing a defense against Arnauld's book, titled Réponse au libelle intitulé La Théologie morale des Jésuites (1644).

Other libels published against Arnauld's Moral Theology of Jesuits included the one written by the Jesuit polemist François Pinthereau (1605–1664), under the pseudonym of the abbé de Boisic, titled Les Impostures et les ignorances du libelle intitulé: La Théologie Morale des Jésuites (1644), who was also the author of a critical history of Jansenism titled La Naissance du Jansénisme découverte à Monsieur le Chancelier (The Birth of Jansenism Revealed to Sir the Chancellor, Leuven, 1654).

In 1655 two very outspoken Lettres à un duc et pair on Jesuit methods in the confessional brought a motion of censorship voted against him in the Sorbonne, in quite an irregular manner.

Twelve years later the so-called "peace" of Pope Clement IX put an end to his troubles; he was graciously received by Louis XIV, and treated almost as a popular hero.

Arnauld gradually evolved away from the rigorous Augustinianism professed by Port-Royal and closer to Thomism, which also postulated the centrality of the "efficacious grace," under the influence of Nicole.

Boileau wrote for him a famous epitaph, consecrating his memory as “Au pied de cet autel de structure grossière Gît sans pompe, enfermé dans une vile bière, Le plus savant mortel qui jamais ait écrit;” ... (“At the foot of this rough structure altar Lies without pomp, locked in a vile casket, The most learned mortal who ever wrote;”) … Antoine Arnauld's complete works (thirty-seven volumes in forty-two parts) were published in Paris, 1775–1781.