BackgroundThe EU bioeconomy strategy aims to accelerate the European bioeconomy and its contributions to the United Nations Sustainable Development Goals and the Paris Agreement. National policies and strategies in many countries promote their bioeconomies. The importance of agricultural crops and residues as raw materials for the bioeconomy is increasingly recognised, but agricultural production also contributes to large impacts on nature and environment. With the aim of assessing the governance measures and their effectiveness in addressing the sustainability of bioenergy and biofuel production, the purpose of this study was to map the governance complex relevant to agricultural crop production in Denmark, and to identify the achievements, challenges and lessons learned.MethodsThe analysis is based on a review and assessment of publicly available databases, inventory reports and scientific literature on governance measures and their effectiveness. Governance here includes a variety of legislation, agreements, conventions and standardisation. Environmental sustainability is represented by greenhouse gas emissions from the agricultural sector, soil carbon, water quality and biodiversity.ResultsThe agricultural sector has a significant impact on Danish climate performance and on landscapes in the form of soil carbon losses, leaching of nutrients to water bodies and pressures on biodiversity. The governance complex addressing these issues is made up of a variety of state regulation and co-regulation between state and firms, state and NGOs, or NGOs and firms. Much regulation is adopted from EU directives and implemented nationally.ConclusionsThe analysis found that greenhouse gas emission is a virtually unregulated field and additional regulation is required to live up to Denmark’s 2030 emission reduction targets. The regulatory framework for soil carbon is criticised for its complexity, its competing instruments and its recognition procedures of voluntary co-regulation. For water quality governance measures in place have improved water quality, but it is still difficult to achieve the goals of the Water Framework Directive. It remains a challenge to protect biodiversity in agriculture. Biodiversity is mainly governed by national and supranational regulation, but co-regulating between state and firms and NGOs and firms have been initiated in the framework of the Agricultural Agreement.