During the Council of Trent (1545–1563), the Roman Catholic Church had reaffirmed, as against Protestantism, both the reality of human liberum arbitrium (free will) and the necessity of grace. Catholicism was then divided into two main interpretations, Augustinism and Thomism, which both agreed on predestination and on efficacious grace, which meant that people cannot resist God's grace, although it did not cancel free will. Augustinism was rather predominant, in particular in the Catholic University of Leuven, where a rigid form of Augustinism, Baianism, was condemned by the Vatican in 1567.
Following the Council, two rival theories emerged in the Church. Under the influence of the ideas of the Renaissance, the newly-founded Society of Jesus asserted the role of free will, with authors such as George de Montemajor, Gregory de Valentia, Leonardus Lessius and Johannes Hamelius (1554–1589). The Jesuit Luis Molina thereafter published in 1588 his treaty De liberi arbitrii cum gratiae donis, divina praescientia, praedestinatione et reprobatione concordia, which stressed that God offers His grace to all people, and that it was by an act of free will that each one accepted it or rejected it. Molina's theology of a sufficient grace became popular, but was opposed by large sectors of the Church who found it incompatible with God's all-mighty powers. The debate between Pelagianism, which underlined humanity's free will, and Augustinism, which insisted on an efficacious grace, was thus revived, opposing Jansenists, who supported Augustinism, to Jesuits who, although clearly not embracing Pelagianism heresy, did insist rather on humanity's free will than on the force of the divine grace. Jesuits thus accepted Augustine's assertion of the necessity of grace, but rejected his conception of it as being infallibly efficient and of being granted to only a small number of elected people. A similar controversy opposed Dominicans to Jesuits, which led Pope Clement VIII to establish the Congregatio de Auxiliis (1597–1607) in order to settle the debate. Although the issue seemed unfavorable to Molinism, the issue finally was suspended rather than solved, with the influence of the Jesuits being one of the reasons for this lack of official condemnation. In 1611 and 1625, a decree from the Holy See prohibited any publication concerning this theme, although it was often informally violated by writings presented as commentaries of Thomas Aquinas.
In 1628, Jansenius, a professor at Leuven, started writing the Augustinus, a bulky treaty on St. Augustine which attempted to conflate Jesuits with Pelagianism by highlighting Augustine's propositions. His complete work was published posthumously, first in 1640 in Leuven, then the following year in Paris and in 1642 in Rouen. Jansenius' publication re-ignited the debate appeased by the Congregatio de Auxiliis. Finally, under the requests of the Brussels' nuncio Stravius and Fabio Chigi, nuncio in Cologna (and future Pope Alexander VII), Pope Urban VIII condemned Jansenius by the In eminenti papal bull in 1642, but in a very general manner and without any particular precision. In France, Cardinal Richelieu himself was strongly opposed to Jansenius, not least because the latter was also the author of a pamphlet against his policies and alliances with German states, titled Mars gallicus (1635). Richelieu therefore charged Isaac Habert, the theologist of Notre-Dame, to preach against Pelagius, while he nominated Alphonse Le Moyne as a professor to the Sorbonne University in order to refutate the Augustinus. However, many theologians of the Sorbonne opposed him, as they mostly followed Augustinism's insistence on efficacious grace. But the Jansenists of the convent of Port-Royal were Le Moyne's and Habert's main opponents. In 1638, Richelieu had its leader, Jean Duvergier de Hauranne, who had been a friend of Jansenius, detained in Vincennes, but this only gave him further influence as a martyr.
After Richelieu's death in 1642, however, the Jansenists were able to reply to the attacks against Jansenius, first by a writing titled the Sanctus Augustinus per seipsum docens, attributed to the Oratorian Colin du Juanet (sometimes to Antoine Arnauld), and then, in 1644-45, by two Apologies pour M. Jansénius (Apologies for Jansenius) by Antoine Arnauld, which enjoyed great success.
In opposition to Jansenism, a little group of theological doctors from the Sorbonne then extracted 8 propositions of Jansenius's Augustinus, later reduced to 5 (in 1649), treating of the problems concerning the relation between nature and grace. They accused Jansenius of having misinterpreted St. Augustine, one of the main Fathers of the Church, conflating Jansenists with Lutherans — in the frame of a highly conflictual context, which had led to the Wars of Religion, officially ended with the 1598 Edict of Nantes. This led Pope Innocent X to condemn on May 31, 1653 these 5 propositions in the Cum Occasione papal bull, and again ten years later. In 1654, the Jansenist Antoine Arnauld replied to this attack by making a distinction between de jure and de facto: de jure, the incriminated propositions could be condemned, and he accepted this sentence; but de facto, they could not be found in Jansenius' treaty. The Sorbonne then attempted to exclude Arnauld from being a theologian. Arnauld was forced underground, while in January 1654 an almanach attributed to the Jesuits grossly presented the Jansenists as under-cover Calvinists. Port-Royal replied to this attack by a poem, titled the Enluminures, written by Louis-Isaac Lemaître de Sacy (author of a French translation of the Bible, called Bible de Port-Royal).
Pascal then wrote the famous Lettres provinciales (1657) in defense of Arnauld, in which he harshly attacked the Jesuits and their morality, in particular casuistry. This led the Holy See to condemn casuistry in 1666 and 1679. Following this anonymous publication, the King sent spies everywhere, condemned the librarians who had clandestinely published the Lettres provinciales and unsuccessfully attempted to discover the author of the Lettres provinciales. The theological debate had turned into a political and theological affair.
On 16 October 1656, Pope Alexander VII again condemned the 5 propositions in the Ad sacram papal bull, specifying that they were condemned "in the sense of Jansenius," but without stating which sense was to be understood. The Jesuits, who then enjoyed predominant political and theological power (including a personal confessor to the King of France, François Annat, and, before him, Nicolas Caussin, while the Cardinal Mazarin strongly opposed Jansenists), both in Europe and abroad (with the Jesuit Reductions and the missions in China) then persuaded the Pope to force all Jansenists to sign a formulary leading them to admit the papal bull and to confess to their faults. The Assembly of the French Clergy hereafter decided to impose on all priests the signature of an anti-Jansenist formulary, in which each one accepted the papal condemnation. One of Pascal's last texts would be the Ecrit sur la signature du Formulaire in 1661 in which he adamantly opposed the signature of the formulary, radicalizing Arnauld's position: Pascal claimed that to condemn Jansenius was equivalent to condemning the Father of the Church Augustine.
The Jansenists of Port-Royal, Antoine Arnauld, Pierre Nicole, la Mère Angélique, Soeur Agnès, etc., were forced to sign the formulary. Although ostensibly obeying to Papal authority, they added that the condemnation would only be effective if the 5 allegedly heretical propositions were in fact found in Jansenius' Augustinus, and claimed that they did not figure there. The Jansenists' reasoning was that the Pope had of course the power to condemn heretical propositions, but not to make that what did not figure in Jansenius' Augustinus be there. This strategy would impose decades of theological disputes and debate, thus allowing them to gain time.
The Lettres Provinciales stimulated several responses from the Jesuits, including in 1657 the publication of an anonymous Apologie pour les casuistes contre les calomnies des jansénistes (Apology of the Casuists Against the Jansenists' Calumnies), written by Father Georges Pirot, which rather unfortunately claimed as its own Pascal's interpretations of the Casuists' propositions, in particular concerning controversial propositions about homicides. This led the friars of Paris to condemn Jesuit casuistry. From then on, the Jansenists of Port-Royal ceased the risky publication of the Lettres Provinciales, and, along with Pascal, started collaborating with the Ecrits des curés (Friars' Writings) which condemned Casuistry. Pirot's anonymous Apology was also condemned by the Holy See, the Vatican putting it at the Index by a decree of Alexander VII of 21 August 1659, while two further decrees, of 24 September 1665 and 18 March 1666, condemned the Casuists' "laxist morality" — Innocent XI issued a second condemnation by a 2 March 1679 decree. In total, the Vatican had condemned 110 Propositions issued by Casuists, 57 of which had been treated in the Provinciales. The books put on the Index in Rome were however published in France, and Jesuits had beforehand bypassed the Holy See's censorship by publishing controversial books there.
On the other hand, Pascal and some other Jansenists adopted a radical strategy, alleging that condemning Jansenius was equivalent to condemning the Father of the Church, St. Augustine himself, and adamantly refused to sign the formulary, with or without reserve. This in turn led to the further radicalization of the King and of the Jesuits, and in 1661 the Convent of Port-Royal was closed and the Jansenist community dissolved — it would be ultimately razed in 1710 on orders of Louis XIV. The controversy did not involve only Papal authority, but rather his authority concerning the interpretation of texts — something Pascal recalled by quoting the Jesuit Cardinal Bellarmin's sentences concerning the authority of religious councils concerning matters of dogma versus de facto issues.