Humanities and social science scholars have recently turned their attention to the embeddedness of microbes in human life as a potential way to decentre the human and thereby decolonise assumptions about the human conquest of the natural world. In this article, I argue that, before such claims can be made, careful historical, regional, and ethnographic analyses of human-microbe relations are needed. My case study of a Japanese sustainable development, agricultural, and environmental NGO shows that human attunement to microbes is not necessarily decolonial in the context of Japan’s modern history. In fact, discourses of human openness to microbial life find affinity with Japanese nationalism and imperialism. Through my analysis, I contribute to scholarship that reveals how environmental visions link up with conservative and right-wing politics.