"Mother of the Goddess' Dormitory" centers around Koushi Nagumo, a high school student who becomes homeless after his father abandons him and their house is repossessed. While wandering the streets, Koushi is discovered by Minerva, a college student who offers him a place to stay. She takes him to Athena Gakuen, an all-girls dormitory where she serves as the dorm mother. Despite initial reservations, Koushi is allowed to stay under the condition that he assists with dormitory chores and maintenance.

The dormitory is home to a group of eccentric and beautiful college students, each with distinct personalities and quirks. Minerva, the kind and responsible dorm mother, takes Koushi under her wing. Atena Saotome, the dormitory's founder and a genius inventor, is often absorbed in her experiments. Serene Hozumi, a shy and reserved girl, struggles with social interactions but forms a bond with Koushi. Freyja Shirogane, a cheerful and energetic athlete, brings liveliness to the group. Kiriya Senshouin, a wealthy and confident young woman, often clashes with others due to her haughty demeanor. Lastly, Sutea Rouka, a mysterious and aloof girl, adds an enigmatic presence to the dorm.

As Koushi adjusts to his new life, he becomes deeply involved in the lives of the dormitory residents. His presence brings a sense of stability and camaraderie to the group, and he gradually forms close relationships with each of the girls. The series explores themes of family, belonging, and personal growth as Koushi navigates his role in the dormitory and the challenges that arise from living with such a diverse group of individuals. The narrative balances comedic moments with heartfelt interactions, highlighting the bonds that develop between Koushi and the residents of Athena Gakuen.