Humanity's growing demands for food, feed, bioenergy and biomaterials put pressure on agroecosystems and the biosphere. If these trends continue, the capacity of agroecosystems to feed the planet while also providing for humanity's energy and material needs is at risk. These demands cause interactions and trade-offs between different biomass uses, competition for biomass and other natural and economic resources. Governing these interactions is difficult, because of the inherent complexity of these interactions but also due to the diversity of biomass resources, the diversity of policy domains and institutions that are needed to govern them. This thesis, therefore, aims to advance the theoretical and empirical understanding of the governance of biomass with the ultimate aim of improving the governance process at the science-policy interface, taking the EU as a case study. By conducting a systematic review, this thesis finds that, overall, the majority of the interactions between food, feed fuel uses of biomass found in the scientific literature are tradeoffs e.g. increasing bioenergy leading to increased resource use consumption as well as higher food prices and land rents. Furthermore, the solutions recommended to address these tradeoffs were diverse, addressing production or consumption of biomass, losses and wastes along supply chains or governance. Each set of solutions set different priorities for biomass, resulting in incoherencies. To dig further into these incoherencies, a policy coherence study was conducted across five policy domains (agro-food, bio-based industry, waste, energy and environment).Utilising a survey and focus groups, this thesis finds that policies are largely considered consistent or synergistic. However, there was considerable uncertainty and context dependencies in the scientific knowledge-base, particularly concerning waste and bio-based industry domains which arise from different incommensurable ways of framing a problem and vagueness which leaves concepts undefined. This thesis examined one such ambiguous concept: the term 'marginal land', a solution that is recommended to overcome competition for biomass between food, feed and fuel uses. Through an analysis of European policies and debates, this thesis finds that the ambiguity around marginal land is a type of uncertainty that results from multiple ways of framing an issue, leaving no clear idea of what is the problem or what should be done about it. Issues of policy incoherence, ambiguity and vagueness can be handled in multiple ways. First, acknowledging the interactions between different policy goals across the different sectors and avoiding 'silo-thinking'.Overcoming vagueness in policies, by having clear definitions where possible, such as having clear cascading guidelines for biomass. Where this is not possible, embracing ambiguity becomes essential. Deliberative approaches are needed where different scientific and policy frames around complex problems can form the starting point. To connect the different perspectives on bioma...