"Moyashimon" centers around Tadayasu Sawaki, a first-year agricultural student at an agricultural university in Tokyo, who possesses a unique ability to see and communicate with microorganisms. These microbes, which appear as cute, anthropomorphic characters, are invisible to everyone else. Sawaki's childhood friend, Kei Yuuki, also enrolls in the same university, and the two become roommates. Kei is aware of Sawaki's ability and often assists him in navigating the challenges it brings.

The narrative explores the daily lives of Sawaki, Kei, and their eccentric classmates and professors as they delve into the world of agriculture, fermentation, and microbiology. The series blends educational content with slice-of-life comedy, offering insights into the science behind food production, fermentation processes, and the role of microorganisms in agriculture. Sawaki's ability becomes a focal point for various experiments and projects, often leading to humorous and unexpected situations.

Key characters include Professor Itsuki, a passionate and somewhat unconventional microbiology professor who takes a keen interest in Sawaki's ability, and Hazuki Oikawa, a senior student with a strong interest in fermentation and brewing. The interactions between the characters are driven by their shared curiosity about the microbial world and their academic pursuits. The series also touches on themes of friendship, personal growth, and the importance of understanding the natural world.

As the story progresses, Sawaki and his friends participate in various university activities, including fieldwork, laboratory experiments, and cultural festivals, all while learning about the intricate relationships between humans and microorganisms. The blend of scientific knowledge and lighthearted storytelling makes "Moyashimon" an engaging and informative series that appeals to viewers interested in both science and everyday life.