Phosphorus (P) and nitrogen (N) are essential for all forms of life. The demand for these nutrients is constantly growing as a result of a rising population. Since the primary production of fertilizers leads to serious environmental impacts, the EU has declared an urgent need to reinvent the farm-to-fork value chain. Flanders is a nutrient-intensive region with a large potential for N and P recycling, especially in concentrated waste streams from livestock production, food processing, and wastewater treatment. The possible recycling technologies that can be used to achieve a more circular economy in this region are manifold. In order to allow decision-makers to plan this transition, the NutriChoice project is going to apply an interdisciplinary approach from the fields of environmental system analyses, socio-economics, and engineering. Novel methods and insights are going to be developed in three areas: i) the elicitation of choice behaviours of actors along the value chain, to quantify the choice variables that shape transition pathways; ii) the development of a prospective technology assessment for N and P recovery; and iii) the development of scenarios (MFA) for N and P in 2050. Conceptual maps, multiple-criteria decision analysis, technology development, technological learning & diffusion, and ex-ante consequential MFA will be used to propose intervention strategies that can effectively reduce the impact of the agro-food system in Flanders.