"Kami-sama Minarai: Himitsu no Cocotama" centers on the concept of Cocotama, tiny divine spirits born from the gratitude of well-loved objects. These spirits, invisible to most humans, inhabit households and assist in maintaining harmony and happiness. The story begins when Kokoro Yotsuba, a fifth-grade girl, accidentally spills juice on her favorite stuffed animal, Shiawase-kun. This act of care and affection causes a Cocotama named Raibaru to emerge from the toy. Raibaru, along with other Cocotama like Kirara, Mekuru, and Mikan, forms a bond with Kokoro, guiding her through everyday challenges while learning about human emotions and responsibilities.

The Cocotama reside in the Cocotama House, a magical space within Kokoro's home, where they train to become full-fledged gods. Each Cocotama has a unique personality and ability, reflecting the object they originated from. Raibaru, for instance, is energetic and determined, while Kirara is elegant and refined, embodying the spirit of a cherished necklace. The series explores their interactions with Kokoro and her family, as well as their efforts to solve problems and bring joy to those around them.

As the narrative progresses, Kokoro and the Cocotama encounter various situations that test their teamwork and understanding. From helping Kokoro with school projects to resolving conflicts among friends, the Cocotama strive to fulfill their duties while growing emotionally. The series also introduces rival Cocotama and challenges that push the characters to develop their abilities and deepen their bonds. Themes of kindness, responsibility, and the importance of cherishing belongings are woven throughout the story, emphasizing the connection between humans and the objects they value.

The episodic structure of the series allows for a mix of lighthearted adventures and heartfelt moments, appealing to a younger audience while maintaining a sense of warmth and charm. The Cocotama's journey to become competent gods mirrors Kokoro's own growth, creating a parallel narrative that highlights the importance of learning, empathy, and cooperation. Through its imaginative premise and relatable characters, "Kami-sama Minarai: Himitsu no Cocotama" offers a wholesome exploration of everyday life infused with magical elements.