The EU Bioeconomy Strategy, updated in 2018, in its Action Plan pledges an EU-wide, internationally coherent monitoring system to track economic, environmental and social progress towards a sustainable bioeconomy. This paper presents the approach taken by the European Commission’s (EC) Joint Research Centre (JRC) to develop such a system. To accomplish this, we capitalise on (1) the experiences ... [Show full abstract] of existing indicator frameworks; (2) stakeholder knowledge and expectations; and (3) national experiences and expertise. This approach is taken to ensure coherence with other bioeconomy-related European monitoring frameworks, the usefulness for decision-making and consistency with national and international initiatives to monitor the bioeconomy. We develop a conceptual framework, based on the definition of a sustainable bioeconomy as stated in the Strategy, for a holistic analysis of the trends in the bioeconomy sectors, following the three pillars of sustainability (economy, society and environment). From this conceptual framework, we derive an implementation framework that aims to highlight the synergies and trade-offs across the five objectives of the Bioeconomy Strategy in a coherent way. The EU Bioeconomy Monitoring System will be publicly available on the web platform of the EC Knowledge Centre for Bioeconomy.