When Pavillon came under royal sanction for his letter protesting Louis XIV's 1664 edict, he set in motion the events that led to the Peace of Clement IX (1669), which ended the formulary crisis. Louis XIV's attempts to discipline Pavillon backfired when a group of French bishops – who had until then supported the king – balked when he asked Pope Clement IX to help him. The pope's role in sanctioning Pavillon and the three other bishops who came to his defense sparked Gallican resistance among other French bishops to the point that Louis XIV feared they might revolt against Rome. To defuse the situation he began negotiations with the pope, the Gallican bishops, and Jansen's defenders. These groups forged a compromise known as the Peace of Clement IX, which ended the formulary crisis by pardoning those who had refused to sign the formulary and silencing the debates over Jansen's text.

The king and pope heralded the Peace of Clement IX as a great achievement, but in reality, the call for silence on Jansen's text did little to secure peace because Pavillon's resistance to Louis XIV's edict of 1664 had already shifted the Jansenist debates away from the five propositions and toward the problem of unfettered royal power in the affairs of the French Church. Fear of this royal power increased during the peace negotiations after Louis XIV nominated Dorothy Perdreau as abbess to Port-Royal-de-Paris in perpetuity.