The region of Flanders in Belgium is, due to its high population density, intensive industry and livestock production, a nutrient-rich region. This results in important anthropogenic emissions to the environment, but also a large potential for the recovery and reuse of nitrogen (N ) and phosphorus (P) from waste streams. In this study, a substance flow analysis study for N and P is presented, in which the anthropogenic fluxes, stocks and hot spots of these two nutrients are quantified throughout the Flemish economy and environment. The environmental impact of the different economic sectors is addressed through the determination of the N and P footprint. The importance of food production in the nutrient cycle is thereby demonstrated through the large contribution of agriculture to the nutrient footprint (49% of N and 36% of P). Further focus is placed on the nutrient use efficiencies across the different sectors of the food supply nexus to target key nutrient losses and inefficiencies. This leads to an overall fertilizer-to-consumer efficiency of 14% for N and P, with the main nutrient losses originating from livestock production and food processing. At the end of the production and consumption chain, important nutrient quantities are embedded in concentrated waste streams such as excess manure, food processing waste streams and activated sludge. This demonstrates the large potential for nutrient recovery as a tool to improve nutrient use efficiencies and reduce the dependency of inorganic fertilizers. Several nutrient recovery strategies, both physicochemical and microbial, were evaluated for their economic feasibility and their impact on the primary energy demand of the total food supply chain.