Julien quickly demonstrates that he is from the countryside when he almost gets into a fight at a Besançon café. He is greeted coldly at the seminary and begins to worry that he has made a mistake. His worry grows to fear when he meets M. Pirard, the director of the seminary. M. Pirard intimidates Julien at first, but when he realizes how intelligent Julien is, he takes him under his wing. This protection proves vital, since Julien's "free thinking" soon makes him many enemies at the seminary.
Julien's time at the seminary allows him to perfect his pious hypocrisy; he pretends to be more religious than any of the other students. As a result Julien becomes even more unpopular, and some priests try to get him turned out of the seminary. M. Pirard defends Julien and allows him to help decorate a nearby church for an upcoming holiday. At the church, Julien runs into Mme. de Rênal, who shrieks and faints at the sight of him. A friend of Mme. de Rênal angrily tells Julien to go away and he obeys. No one else notices this exchange.
Back at the seminary, M. Pirard, impressed with Julien's conduct, promotes him to the post of tutor. This encourages the jealousy of the other priests, who attempt to flunk Julien during his exams. Disgruntled with the politics of the seminary, M. Pirard resigns. With the help of a Parisian benefactor, the Marquis de la Mole, Pirard moves to Paris. The Marquis wants Pirard to be his personal secretary, but Pirard recommends Julien in his place.
Before leaving for Paris, Julien returns to Verrières to see Mme. de Rênal one last time. She tries to send him away but gradually gives in to temptation and lets Julien spend the night with her. Julien discovers that M. Pirard had been intercepting letters from Mme. de Rênal, but they both remain committed to each other. He hides under her bed for a day, and it is only when M. de Rênal thinks there is a thief in the house that Julien jumps from Mme. de Rênal's window and heads for Paris.
Despite virtuous characters like M. Chélan and M. Pirard, Stendhal presents a negative image of the Church in this section. The different priests who teach at the seminary are most concerned with their different political allegiances and are constantly back-stabbing each other. The students are largely uneducated peasants who want to become priests only to make money. The seminary is also divided along class lines: Julien is singled out for being a well-educated bourgeois. Stendhal indicates that the Church is a microcosm of the political instability of France. Sincere public servants like Chélan and Pirard are manipulated out of office by reactionary and conservative-minded priests. Although Stendhal was raised in a religious family, he does not hesitate to condemn the Church, and thus France, for its rampant corruption and greed.
Julien gains M. Pirard's trust and support, but continues to rely on hypocrisy to get ahead. He lies to Pirard about the amount of money he has with him, as well as about a woman he met at a café. He also pretends to be more devout than he actually is, taking pride in his "most interesting acting." Julien's ability to get ahead in the seminary by being what his superiors expect him to be foreshadows his later success in Paris.
The Marquis de la Mole hopes that M. Pirard will lend legitimacy to a court case the Marquis is fighting, but has heard of Julien's (good) reputation and gladly accepts him instead. Stendhal emphasizes this relationship between the Marquis and M. Pirard in order to expose the strong ties between the aristocracy and the Church. In effect, M. Pirard hints to the Marquis that Julien is the illegitimate son of a nobleman. Julien's intelligence and "devotion" to the Church is thus falsely explained to be the result of an aristocratic birth.
Julien gladly accepts the position in Paris, seeing it as proof that he is moving up in the French society. He feels that his reliance on hypocrisy will pay off in the "theater of the world." In fact, his move to Paris symbolizes a distinct shift in his wavering between the red and the black. Even though he is supposed to continue his ecclesiastical studies in Paris, he plans on living like an aristocratic soldier. This is shown in his visit to Mme. de Rênal: he climbs to her window with a ladder, hides under her bed, and dodges the bullets of a servant who mistakes him for a thief. This foray into knight-like chivalry prefigures his adventures in Paris.