"Otaku Elf" centers on the life of Elda, an ancient and powerful elf who has been revered as a deity in Japan for centuries. Despite her divine status, Elda is an unapologetic otaku, deeply engrossed in modern pop culture, particularly video games, anime, and manga. She resides in a shrine in Tokyo, where she is attended by her loyal shrine maiden, Koito Koganei. Koito, a diligent and responsible young woman, struggles to manage Elda's eccentric behavior and her obsession with contemporary hobbies, which often leads to comedic and chaotic situations.

The narrative explores the dynamic between Elda and Koito as they navigate their daily lives. Elda's refusal to conform to traditional expectations of a deity creates frequent misunderstandings and challenges for Koito, who must balance her duties with the elf's unpredictable antics. Despite their differences, the two share a genuine bond, with Koito often finding herself drawn into Elda's world of gaming and fandom. The series humorously contrasts Elda's ancient wisdom and magical abilities with her childlike enthusiasm for modern entertainment, highlighting the clash between tradition and modernity.

Throughout the story, various characters interact with Elda and Koito, including other shrine maidens, townspeople, and even supernatural beings. These interactions further emphasize the cultural and generational gaps between Elda's timeless existence and the rapidly evolving world around her. The series blends comedy, slice-of-life elements, and light fantasy, offering a unique take on the isekai and fantasy genres by grounding its fantastical premise in relatable, everyday scenarios. Elda's growth as a character is subtly woven into the narrative, as she begins to understand the responsibilities of her role while remaining true to her otaku passions. Koito, in turn, learns to appreciate the value of balance and adaptability, making their relationship a central pillar of the story.