Megami no Café Terrace follows Hayato Kasukabe, who returns to the seaside family café after the death of his grandmother, Sachiko, only to discover that Familia Café Terrace has become the home of five girls who were taken in by her: Ouka Makuzawa, Akane Hououji, Riho Tsukishima, Shiragiku Ono, and Ami Tsuruga. Hayato originally intends to demolish the property and turn it into a parking lot, but the girls refuse to let the place that sheltered them disappear, forcing him to confront a future he never planned.
Living under the same roof, Hayato is drawn into the daily rhythm of the café and the complicated bonds among the five girls, each of whom carries her own personality, ambitions, and feelings for the place Sachiko left behind. What begins as a conflict over an inheritance gradually turns into a story about responsibility, memory, and rebuilding a home that matters to everyone involved.
As Hayato reflects on his past with Sachiko, he starts to understand the warmth and legacy tied to Familia Café Terrace. Determined to preserve that legacy, he changes course and asks the five girls to work with him as the "goddesses" who can keep the café alive.