Every year 120–140million tonnes of bio-waste are generated in Europe, most of which is landfilled, incinerated or stabilized and used as covering material in landfill operation. None of these practices enables the recovery of essential nutrients such as phosphorus (P) and nitrogen (N), which are in great demand for agricultural production. Recovery of these nutrients is a matter of international concern considering the non-renewable nature of P sources and the energy intensive production process required for the synthesis of N fertilizers. The objective of this research is to understand the relation between the municipal solid waste management (MSWM) system, both its the physical components and governance aspects, and the recovery of nutrients in Vitoria-Gasteiz (Basque Country) as a benchmark for European medium-size cities. The analysis shows that the existing physical infrastructure and facilities for bio-waste have high potential for nutrient recovery, 49% for N and 83% for P contained in bio-waste. However, governance aspects of the MSWM system such as legislation and user inclusivity play an important role and decrease the actual nutrient recovery to 3.4% and 7.4% for N and P respectively.