Urban development trajectories in sub-Saharan Africa are unsustainable. Fast-growing cities constitute nutrient sinks relying on nutrient-poor hinterlands. We propose a pragmatic waste flow assessment providing authorities with a cross-sectoral view of a city’s nutrient sink status. Following a nested approach, we focus on the origin and fate of a city’s nutrient-containing waste flows, constituting a partial urban metabolism. Application of this method for nitrogen to Maradi, Niger, and Ouagadougou, Burkina Faso, shows that the city of Maradi is a nitrogen sink in a still rather sustainable city region food system. Maradi’s Territorial Sustenance index, expressing net N provision from within the territorial system as a share of urban throughput, is around 79%. But Maradi may well be set to evolve towards a situation similar to that of Ouagadougou: a large nitrogen sink with no significant city-hinterland recycling. Ouagadougou exhibits a Territorial Sustenance index of about 5%. Urination constitutes the dominant nitrogen loss pathway and urine-collecting initiatives could provide valuable fertilizer adapted to local agricultural requirements and constraints, increasing the urban system’s sustainability by enhancing regional food provision as well as by reducing sanitationinduced urban water pollution.