Launched in 2012, the Bioeconomy Strategy of the European Commission aims at developing the production and use of biomass within the European Union as a strategy to limit the consumption of fossil carbon while fostering jobs and growth. The quantification of biomass flows and their timely reporting are crucial for the monitoring of such strategy. In this framework, the present study focuses on the quantification of primary agricultural residues in the European Union as a promising feedstock for the bio-based and bioenergy sectors. Harvest indices or residue-to-product ratios (RPRs), determined at crop level, usually enter the computation of primary agricultural residues. Comparing four different functional forms of RPRs in function of the level of crop yield, we show that exponential forms better simulate the production of crop residues for high levels of annual crop yields. We then complement the RPRs reported in the scientific literature with twenty two exponential forms of RPRs and four fixed RPRs for commodities (or group of commodities) not reported so far. Finally, we estimate that 395 million tonnes of dry matter (Tdm) of primary agricultural residues are produced in Europe in 2013 from more than 130 crop commodities. Out of them, 297 million Tdm should remain in the fields for the maintenance of ecosystem services (using conservative assumptions) and 37 million tonnes are collected for agricultural uses. Hence, 62 million Tdm are collectable as feedstock for the bio-based and bioenergy sectors. They are mainly composed of cellulose (58%) and sugar and starch (11%). The production of primary agricultural residues is concentrated in the major cereal producing countries and stable over time. Nevertheless, a wider adoption of ad’hoc harvesting machinery, the optimisation of logistic processes and the maturation of the new bio-based value chains could help to better take advantage of the current production of agricultural residues.