This study analyses the sustainability transitions of technological innovation systems (TISs) in the context of multi-level governance frameworks. TISs which are spatially embedded in both international and national arenas are simultaneously governed by the governance frameworks in different layers, i.e. international institutions on a macro level, national institutions on a meso level and domestic dynamics of novel technologies on a micro level. Through the investigation of the biodiesel innovation system in Taiwan, this study concludes that international institutions could appropriately play a role in the guidance of search, while national governments should ensure policies are consistent and generate appropriateness on the domestic TISs' functions. If the domestic TISs’ functions are appropriately guided by the institutions on the above levels, novel technologies that sustainably transit the systems would then emerge on a micro level.