This paper draws on two case studies from India and China to discuss how and why rapidly urbanizing contexts are particularly challenging for transformative innovation but are also critical sustainability frontiers and learning environments. We argue that lack of understanding and policy engagement with peri-urbanization in its current form is leading to increasing exclusion and unrealized potential to support multiple sustainable urban development goals. Peri-urbanization is often characterized by the neoliberal reordering of space and a co-option of environmental agendas by powerful urban elites. Changing land-use, resource extraction, pollution and livelihood transitions drive rapid changes in interactions between socio-technical and social-ecological systems, and produce complex feedbacks across the rural–urban continuum. These contexts also present characteristic governance challenges as a result of jurisdictional ambiguity, transitioning formal and informal institutional arrangements, heterogeneous and sometimes transient communities, shifts in decision making to distant authorities and the rapid growth of informal market-based arrangements with little incentive for environmental management. These unique features of peri-urbanization may reinforce a lack of inclusion and hinder experimentation, but they can also present valuable opportunities for transformative innovation. This innovation is unlikely to follow the lines of niche management and upscaling but rather should take advantage of peri-urban dynamics. There are possibilities to build new alliances in order to renegotiate governance structures across the rural–urban continuum, to reframe urban sustainability debates and to reconfigure socio-technical and social-ecological systems interactions.