To date, most debates about transdisciplinarity (TD) have been dominated by Western institutions. This paper proposes insights from the Research Institute for Humanity and Nature (RIHN), Kyoto, Japan, from an investigation as a visiting scientist. After describing its unique project-based organization, I first show that the development of TD at RIHN faces some common challenges, such as TD evaluation, education and upscaling (beyond local contexts). Yet, collaborations with stakeholders have also unique specificities (importance of the group, rigidity of institutions, different ways of interacting…). Moreover, most RIHN researchers claim to have a particularly practical approach to TD. At the level of the whole institute, RIHN gives a strong emphasis on the premise that environmental problems are rooted in human cultures and values. RIHN also develops a specific approach to scales, in which Asia serves as a nodal point between the local and global (‘Asia vision’). We suggest that RIHN’s emphasis on cultural roots and its nodal approach to scale might be themselves rooted in the Japanese culture.