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The bioeconomy is nowadays widely proclaimed by governments and corporations around the world as a new paradigm for a sustainable economy. Essentially, it broadly denotes the promotion, development and establishment of the use of biogenic resources in diverse kinds of industrial technologies, production processes and products. Yet, in order for the bioeconomy to be sustainable, it has to be assured that these biogenic resources are sourced sustainably. In the last 30 years, transnational sustainability certification (TSC) has established itself as a popular instrument in this context, for example in the case of European biofuels sustainability regulation. In the last decade or so, however, TSC initiatives in several biomass production sectors like palm oil, soy, fruits, aquaculture or fisheries—mostly initiated by non-governmental organizations (NGOs) and corporations from the Global North—are increasingly met with resistance from actors from the resource-producing countries, mostly located in the Global South. Issues brought up in this context concern their lack of legitimacy and respect for national regulatory sovereignty and conflicting priorities in terms of sustainable development. Consequently, governmental and corporate actors from the resource-producing countries have developed sustainability standards that now at least partly compete with TSC. Against this background, this contribution investigates this apparent dilemma of biomass certification by taking stock of existing TSC initiatives and territorial responses to them in several sectors of the bioeconomy in order to discover general patterns and dynamics of transnational biomass sustainability certification. This analysis is based on a review of existing empirical studies on these issues as well as on conceptual literature on discourse coalitions and transnational hybrid governance for the classification of the different aspects and developments in the individual sectors. Results show that TSC is indeed challenged in all sectors around story lines of sovereignty and sustainability, employed by closely associated state and industry actors in the specific context of the prevalent state-industry relations and the practices and institutions of the respective international political economies. Beyond this general pattern, these alternative systems take on different shapes and complex relations between transnational and territorial sustainability governance emerge that are not always antagonistic, but also exist in parallel or even complementarily and involve various hybrid configurations of public and private actors. Overall, this casts some doubt on the potential of TSC as an instrument to safeguard the sustainability of the bioeconomy and shows one of its potential pitfalls, which is reflected upon in the conclusion.