Identifying pathways to circular agriculture requires a profound understanding of nutrient flows and losses throughout the food system, and of interactions between biophysical conditions, land use, food production and food consumption. We quantified nitrogen (N) and phosphorus (P) flows of the food system of the North-Netherlands (NN) region and of its 30 subregions varying in biophysical and socio-economic conditions. The food system included agriculture, food processing, consumption, and waste processing. Nitrogen use efficiency (NUE), phosphorus use efficiency (PUE) and the nutrient cycling counts were calculated. Results show a low NUE (25%) and PUE (59%) of the food system. External inputs were used to maintain high yields and production. Nutrient cycling was very limited with losses from agriculture ranging from 143 to 465 kg N ha−1 y−1 and 4 to 11 kg P ha−1 y−1. Food system losses ranged from 181 to 480 kg N ha−1 y−1 and from 7 to 31 kg P ha−1 y−1 and varied with biophysical conditions, population density and farming systems. Large losses were associated with livestock farming and farming on drained peat soils. Food system efficiency was strongly associated with the utilization of produce. We conclude that increasing circularity requires tailoring of agriculture to local biophysical conditions and food system redesign to facilitate nutrient recycling. Steps towards circularity in NN include: matching livestock production to feed supply from residual flows and lands unsuitable for food crops, diversifying crop production to better match local demand and increasing waste recovery.