Organic agriculture (OA) is the promoted sustainable agriculture model in the European Union (EU), yet its expansion is hindered by limited nutrient availability, particularly nitrogen (N). OA’s main sources of N include biological N fixation by legume crops and manure from both conventional and organic livestock. However, potential stricter EU regulations on allowed external N resources for OA and pressure to reduce livestock numbers could impact N availability in OA. Understanding national-scale N flows is essential. Here, we analysed N flows in organic agri-food systems in France, the largest OA area in Europe. We show that approximately 20 % of the manure used to fertilise organic cropland came from conventional agriculture and 15 % from the dietary N nutritional requirements of organic livestock imported from outside France. N surplus is half that of the conventional agriculture at national scale. This first national assessment highlights biophysical and regulatory constraints providing insights into the possibilities of achieving the EU’s target of having 25 % of agricultural land under OA.