This chapter addresses the fate of nutrients in agro-food systems after their ingestion by humans. Depending on how human urine and faeces are managed, they can become a source of pollution to the environment, or they can be used as a resource, notably as fertilisers, thus contributing to closing the loop of nutrients. Taking the city of Paris as a case study from the nineteenth to the twenty-first century, we analyse the fate of human excreta through the evaluation of corresponding nitrogen and phosphorus mass flows. We put forward two major phases concerning the management of human excreta : 1. The circularisation phase (1800s to 1900s): human excreta management is characterised by increasing circularity which peaks in the 1900s with around 50% of human excreta nutrients being recycled. 2. The linearisation phase (1900s–today): human excreta management is characterised by increasing linearity, i.e. a decrease in recycling rates of nutrients. Generalisation and improvement of wastewater treatment have led to decreasing pollution but also confirm the linearisation process (e.g. 5% recycling of human excreta nitrogen). This increase in linearity came together with increased dependency of agro-systems on fossil resources. Ongoing climate change is also putting the current system under pressure since the dilution capacity of the Seine River is decreasing, while the population of Paris is increasing. We therefore analyse three scenarios of future human excreta management (incineration, end-of-pipe recycling and source separation) and show that source separation of human excreta may offer the perspective of a sustainable human excreta management system.