The Ministry of the Environment of Japan reports that most environmental education in Japan lacks substantial action. The interviews we conducted with primary school teachers also revealed that limited space, time, and teaching materials make it difficult for them to implement effective environmental education. To address these issues, this study aims to design a fermentation kit named NIKO (Nuka In Koji Out) and to explore its potential as a tool for promoting environmental education and awareness of non-human beings in daily life. This kit is designed to engage families with children in the process of making rice koji, a traditional Japanese fermented food, and encourages them to interact with invisible microorganisms and begin to think of themselves as part of the ecosystem. The prototype of the NIKO fermentation kit was based on the Design Research Through Practice methodology, which involves hypothesis from literature review and interviews, experiment, analysis, and evaluation. Before and after the workshop, as well as 1 month later, participants completed a questionnaire about their awareness and behavioral changes. Based on the survey results, the fermentation kit workshop was found to be a positive experience for participants, including children, who expressed a sense of joy in making something from scratch and an increased affection for the world of microbes. This research results suggest that the fermentation kit has the potential to provide an effective and engaging way to raise awareness of the importance of microorganisms in daily lives and to introduce environmental education to families with children in Japan.