In 17th-century Pescia, Italy, a young girl named Benedetta Carlini is brought by her parents to a Theatine convent overseen by Abbess Felicita (Charlotte Rampling). After 18 years of devoted life, during a play where she plays the Virgin Mary, the adult Benedetta (Virginie Efira) experiences a profound vision of Jesus calling her name.
Things take a turn when Bartolomea (Daphné Patakia), a teenage peasant girl, seeks refuge in the convent from her abusive father. Benedetta is tasked with guiding Bartolomea as she adjusts to convent life. That night, a passionate kiss from Bartolomea ignites something deeper within Benedetta. As time passes, Benedetta begins having vivid visions of Jesus. After a traumatic vision where a man she believes to be Jesus saves her from a brutal attack, she falls gravely ill. Abbess Felicita assigns Bartolomea to care for her during this distressing time.
During further visions, Christ urges Benedetta to undress and touch His hands. To her bewilderment, she wakes up the following morning with stigmata on her hands and feet, sparking an investigation into these miraculous occurrences. Abbess Felicita becomes skeptical, noting that Benedetta's stigmata manifested while she was asleep, not in prayer, and her forehead lacks the marks of a crown of thorns. Shortly after, Benedetta collapses outside Felicita's chambers and begins speaking in a commanding male voice, chastising those who doubt her while fresh wounds appear on her forehead.
Sister Christina (Louise Chevillotte), the abbess's daughter, suspects foul play after discovering a shard of pottery nearby, raising concerns about Benedetta's wounds. A conflict brews between Felicita and local church authorities regarding how to handle the looming fascination surrounding Benedetta's visions, eventually leading to Benedetta's rise to abbess, replacing Felicita. As Benedetta and Bartolomea take residence in Felicita's former quarters, they begin a steamy romance, even resorting to using a dildo that Bartolomea crafts from Benedetta's wooden Virgin Mary statuette.
During confession, Christina lies to a priest, claiming she witnessed Benedetta inflicting her own wounds, forcing the priest to compel her to speak publicly about her accusations. Nevertheless, Abbess Felicita defends Benedetta, revealing that Christina previously admitted she hadn't seen the acts occur. In a twisted turn of fate, Benedetta, seemingly inhabited by Jesus's spirit, orders Christina to flagellate herself while Felicita spies on Benedetta and Bartolomea engaging in their passionate affair.
In despair from her humiliation, Christina tragically jumps to her death from the convent’s roof. As a deadly plague sweeps through the area, Benedetta proclaims that Pescia will be spared, ordering the abbey to be closed to avoid contamination. In a covert mission, Felicita journeys to Florence to disclose Benedetta's indiscretions to the papal nuncio, while Benedetta succumbs to a mysterious ailment.
Upon Felicita's return with the Nuncio (Lambert Wilson), Benedetta miraculously revives, claiming she experienced heaven and learned the fates of all present. As a representative of the Pope, the Nuncio launches an investigation into Benedetta's behavior. Initially, Bartolomea denies any sexual involvement but eventually breaks under torture, leading the Nuncio to uncover the wooden dildo hidden within a Bible. He orders Benedetta’s arrest, during which she again speaks in a male tone, prophesying the Nuncio’s impending illness.
Chaos ensues in the town square when Benedetta is set to be executed by burning at the stake. Just before the flames engulf her, she reveals new stigmata, asserting that the Angel of Death is near. In a dramatic revelation, Felicita, afflicted by the plague, blames the Nuncio for bringing calamity upon Pescia. The townspeople revolt, preventing Benedetta’s execution and leading to the Nuncio’s demise at their hands.
In the midst of the upheaval, Bartolomea frees Benedetta, discovering a bloody potsherd beside her. Escaping the chaos, the two women flee the town, while Felicita chooses to end her life by self-immolation upon the pyre meant for Benedetta.
The film concludes with Benedetta, after a night spent with Bartolomea, resolutely returning to the convent despite her companion’s pleas for her to stay and confess the truth about her stigmata. A title card notes that Benedetta lived until 1661 in the abbey, outlasting the plague that spared Pescia.
