The relationship between European trade and biodiversity is complex and multifaceted. Trade flows impact biodiversity both directly and indirectly, and are dependent on ecosystem services that are underpinned by biodiversity. Evidence shows that global trade flows currently contribute to substantial environmental pressures and associated biodiversity loss. This also implies that gains can be made for biodiversity if these pressures are reduced or removed. Environmental provisions are increasingly being included in trade policies and agreements to achieve this, but their effectiveness is constrained by a poor understanding of biodiversity-trade interactions and effects, and a lack of measurable metrics and targets. Moreover, environmental policies aimed at mitigating the adverse effects of trade often risk merely re-directing trade flows, and the associated environmental pressures, to other regions. The challenge of understanding and addressing the effects of trade, environment and biodiversity interactions is further exacerbated by siloed analytical and policy domains dealing with trade.We present a research agenda that synthesises insights from diverse scientific disciplines, policy sectors, and recent scholarly advances in biodiversity and trade. The research agenda was developed through an iterative process that drew on Delphi methodologies to gather input and expertise from the Partnership for European Environmental Research (PEER), a network of eight leading environmental research institutes across Europe. This was combined with inputs from a workshop with policymakers, particularly from the European Commission. Although our research agenda draws on examples of global trade with the European Union (EU), the identified research topics apply generally to global trading systems.The proposed research agenda comprises four research topics: two aimed at understanding the effects of biodiversity-trade interactions, and two focused on responses that reconcile biodiversity outcomes in trading systems. In the first two, on understanding the effects of biodiversity-trade interactions, we highlight the need for complex systems analysis that takes account of a diverse range of disciplines and includes a deeper examination of the underlying causes of ecologically harmful trade. In the second, on considering responses to improve biodiversity outcomes in trading systems, two key topics of research were identified: the first topic focuses on financial flows and supply chains, and the second on effective and equitable policies for the biodiversity-trade nexus. Together, the four research topics provide information to critically assess where and under what conditions trade can be beneficial from a broader societal perspective – a perspective that accounts for a range of environmental, social and economic outcomes across geographic scales, sectors and social groups. With this research agenda we aim to foster critical inquiry, interdisciplinary and transdisciplinary collaboration, and science-policy initiatives that enhance the knowledge, data and capacities necessary for a more sustainable and equitable approach to global trade and biodiversity governance.