The region of Flanders in Belgium has due to its high population density, intensive livestock production and industry a nutrient surplus available in waste streams. It therefore possesses a large potential towards the recovery and reuse of nitrogen and phosphorus. In this study, a substance flow analysis study for nitrogen and phosphorus is presented, in which the fluxes, stocks and hot spots of both nutrients are quantified throughout the economy. The predominant nutrient fluxes are found within the food supply chain, which connects industry, agriculture and consumption. This food supply chain revealed a fertilizer-to-consumer efficiency of 14% for N as well as for P. At the end of the production and consumption chain, a total of 17 kg N cap-1 yr-1 and 8.3 kg P cap-1 yr-1 of nutrients ends up in waste streams. Only a fraction of these nutrients (17% of N and 12% of P) is currently recycled. Several nutrient recovery strategies, both for chemicals and single cell protein production, were therefore evaluated for their economic feasibility and their impact on the energy demand of the food supply chain.