Benedetta explores the passionate lesbian relationship between two nuns in a 17th-century Italian convent. The film depicts their intimacy and desires with complexity and agency, intertwining their spiritual and physical connection. While they face severe persecution from the Church, the narrative frames these obstacles as external societal forces, maintaining an empathetic stance towards their queer identity and affirming the worth of their bond.

The narrative centers on a lesbian relationship between two nuns, normalizing sexual freedom and challenging traditional religious authority within a chosen community. The film critiques established norms rather than endorsing traditional family values or structures.

The film depicts the Catholic Church as a deeply corrupt and hypocritical institution, driven by power, greed, and the suppression of individual agency. It highlights the abuse of authority, sexual repression, and the exploitation of faith for personal gain within the convent. The narrative critiques the systemic failings and human corruption operating under the guise of religious devotion.