The monk Athanaël returns to his religious brethren from Alexandria. He tells Palémon, the leader of the congregation, and his colleagues how shocked he was to find the city immersed in sin. Athanaël blames this spiritual disorder on the beautiful courtesan Thaïs. Athanaël recalls seeing her in the years before he had taken his vows.
When the monks retire, Athanaël lies awake and has a vision of Thaïs. He determines to return to Alexandria to try to convert the courtesan, despite Palémon’s warnings not to meddle in other people’s lives.
Athanaël visits his friend, Nicias, who has paid a fortune to spend a week with Thaïs. Nicias laughs at the monk’s plan, but agrees to introduce him to Thaïs, who will soon be arriving for her final night with Nicias. When she appears, she notices the monk staring at her, but dismisses his sermon. Athanaël tells her that he will come to her house the next day with the promise of salvation.
Thaïs gazes into her mirror, wondering what will happen when her beauty fades. Athanaël arrives and tells that her that the love he offers brings the blessing of eternal life and freedom from sin. Although she is fascinated by his message, the spell is broken when she hears Nicias’ voice outside, reminding her of her past. Torn between her current life of luxury and the promise of redemption, she collapses in despair. Athanaël goes outside to await her decision. Throughout the night, Thaïs meditates and prays alone.
The next morning, Thaïs is ready to follow Athanaël’s path to holiness. He tells her that she must set fire to her house and burn all of her worldly possessions. She agrees, hoping only to retain a statue of Eros given to her by Nicias, but Athanaël angrily destroys it. Outside, when Athanaël announces that Thaïs has consecrated herself to God, the crowd turns violent at the thought of losing her. To distract them, Nicias throws money at the mob. Thaïs and Athanaël flee to safety as her house erupts in flames.
On their journey to Mother Albine’s convent, Thaïs and Athanaël stop to rest at a desert oasis. Exhausted, she can barely walk. The monk explains that she must endure this suffering to rid herself of sin, but when he sees that her feet are bleeding, he comforts her. Arriving at the convent, Athanaël realizes that he will never see her again.
He returns to his brethren, but cannot stop thinking about Thaïs. In dreams, he first sees her as a temptress, then sees her dying. When he wakes, he decides that he must go to her.
After three months of penance, Thaïs is weak, but in the loving care of the nuns who pray for her. Albine welcomes Athanaël, who kneels before Thaïs and confesses that his love for her is now physical desire. In a state of mystical ecstasy, she does not understand him. She dies in peace and happiness, as Athanaël begs God’s mercy.