"Kami-sama Minarai: Himitsu no Cocotama" centers around a young girl named Kokoro Yotsuba, who discovers a hidden world of tiny deities known as Cocotama. These deities are born from the gratitude of inanimate objects that have been cherished by their owners. Kokoro’s life changes when she accidentally spills ink on her grandmother’s old notebook, leading to the birth of her first Cocotama, RaKuma. RaKuma, along with other Cocotama like Miime, Gurt, and Kiraru, reside in Kokoro’s home and assist her in their training to become full-fledged gods.

The Cocotama are invisible to most humans, but Kokoro can see and communicate with them due to her pure heart and kind nature. Each Cocotama has a unique personality and abilities tied to the objects they originate from. RaKuma, born from the notebook, is studious and responsible, while Miime, born from a mirror, is vain but caring. Gurt, originating from a comb, is energetic and playful, and Kiraru, born from a light bulb, is shy but bright. Together, they navigate the challenges of their training, often learning valuable lessons about responsibility, kindness, and the importance of gratitude.

The narrative unfolds through episodic adventures, with Kokoro and the Cocotama helping others in their community while balancing everyday life. The Cocotama often intervene in small but meaningful ways, such as fixing broken items or resolving misunderstandings, emphasizing the theme of appreciating the little things in life. As the series progresses, Kokoro’s bond with the Cocotama deepens, and they collectively grow, learning to overcome obstacles and strengthen their abilities.

The story also introduces other characters who interact with the Cocotama, including Kokoro’s friends and family, who remain unaware of the deities’ presence. The Cocotama’s existence is kept secret, adding an element of whimsy and mystery to the series. Through its lighthearted and heartwarming tone, "Kami-sama Minarai: Himitsu no Cocotama" explores themes of friendship, gratitude, and the unseen magic in everyday life, appealing to a younger audience while maintaining a universal charm.