Resource-efficient nutrient management is key to secure food production in the context of a growing global population, rising resource scarcity and increasing pressure on the environment. To map the potential towards increasing nutrient use efficiencies and reduce environmental losses, a high-resolution insight of the nitrogen (N) and phosphorus (P) nutrient streams is pivotal. In this study, a substance flow analysis for N and P is presented for the nutrient intensive region of Flanders (6,211,065 inhabitants) in Belgium for the year 2009. A set of 160 nutrient fluxes was quantified throughout 21 economic and environmental compartments, with a particular focus on 10 waste management processes. A total nutrient load of 20 kg N cap−1 yr−1 (ca. 73% to the air and 28% to surface waters) and 0.53 kg P cap−1 yr−1 (to surface waters) is emitted to the environment; with crop and livestock production as the main contributors (49% of N and 36% of P). The food supply chain revealed a fertilizer-to-consumer efficiency of 14% for N as well as for P, with important losses embedded in waste streams such as excess manure. Advanced manure and waste processing facilities nevertheless offer the opportunity for enhanced nutrient recycling to increase the nutrient use efficiencies and reduce the dependency of inorganic fertilizers.