In 17th-century Pescia, Italy, a young Benedetta Carlini (Elena Plonka) is enrolled by her parents in a Theatine convent run by Abbess Felicita (Charlotte Rampling), to become a nun. 18 years later, while playing the Virgin Mary in a play, the adult Benedetta (Virginie Efira) has a vision of Jesus calling to her. One day, a young teenage peasant woman named Bartolomea (Daphné Patakia) seeks shelter in the convent from her abusive father. Benedetta is assigned to oversee Bartolomea's integration into convent life. That night, Bartolomea kisses Benedetta.Benedetta begins to have recurring visions of Jesus. After a particularly fraught vision, where a man whom she mistakes for Jesus saves her from being gang raped, Benedetta falls into a deep illness. Abbess Felicita assigns Bartolomea to look after her. Benedetta has another vision of Christ, asking her to undress and touch his hands. The next morning, she wakes up with stigmata on her palms and feet.An investigation ensues. Abbess Felicita is skeptical because Benedetta's stigmata appeared while she was asleep, not during prayer, and her forehead lacks the marks of a crown of thorns. Outside Felicita's chambers, Benedetta collapses. She then begins speaking in an angry male voice, castigating those who doubt her, as bleeding wounds appear on her forehead. Sister Christina (Louise Chevillotte), Felicita's daughter, suspects that Benedetta's wounds are self-inflicted, after spotting a nearby shard of pottery.Following a dispute between Felicita and local church leaders about the way popular interest in Benedetta's visions should be handled, Benedetta is elevated to the position of abbess in place of Felicita. Benedetta and Bartolomea move into Felicita's old quarters and they soon begin a sexual relationship. Later for sex, they use a dildo carved by Bartolomea out of Benedetta's wooden Virgin Mary statuette.In confession, Christina lies to the priest that she witnessed Benedetta inflicting her forehead wounds. The next day, the priest compels Christina to say her accusations publicly. When questioned by the priest, Felicita refutes Christina's claims because Christina has previously admitted to her that she did not actually see the wounds being self-inflicted. Benedetta, apparently possessed by the spirit of Jesus, orders Christina to flagellate herself. Felicita later observes Benedetta and Bartolomea having sex through a peephole in their chambers.Humiliated, Christina jumps to her death from the roof of the convent. As a plague begins to ravage the countryside, Benedetta has a vision that Pescia will be spared and orders the abbey closed to prevent infection. Felicita secretly travels to Florence to report Benedetta's sexual indiscretions to the local papal nuncio. Meanwhile, Benedetta suddenly dies of unknown causes.Shortly after Felicita returns to the abbey with the Nuncio (Lambert Wilson), Benedetta revives, saying that she was in heaven from her near-death experience and has seen the fates of all those present. The Nuncio, as representative of the Pope, opens a court of inquiry into Benedetta's conduct. Bartolomea initially denies any sexual involvement with Benedetta, but after being tortured by the Nuncio's men, she ultimately confesses the truth, leading the Nuncio to the wooden dildo hidden in a bible. He has Benedetta arrested; speaking in a male voice again, she lashes out at those who persecute her, announcing that the Nuncio will soon fall ill. The Nuncio discovers that Felicita has the plague and orders her condition to be hidden. Bartolomea is expelled from the abbey.In the town square, before she is to be executed by being burned alive, Benedetta reveals new stigmata and, speaking in a male voice, announces that the Angel of Death approaches. Felicita, revealing her disease, blames the Nuncio for bringing the plague to Pescia. Chaos ensues as the townspeople prevent the Nuncio's men from burning Benedetta at the stake. Bartolomea unties Benedetta, discovering a bloody potsherd at her feet. As the Nuncio is killed by an angry mob, Benedetta and Bartolomea flee from the town, and Felicita self-immolates herself on the bonfire lit for Benedetta's execution.In an abandoned stable outside of town, after spending the night with Bartolomea, Benedetta insists that she must return to the convent. Bartolomea begs her to stay and tries to get her to admit that she faked her stigmata, but Benedetta refuses and instead heads back towards Pescia.A title card reveals that Benedetta lived in the abbey until her death in 1661 at the age of 70, and that the plague spared Pescia.