Phosphorus is a finite resource that is in high demand due to its essential role as a fertiliser. We undertook a substance flow analysis of phosphorus for India’s agri-food system to identify where the biggest losses of phosphorus occur and which flows could be targeted to move phosphorus from a linear use and waste approach to a circular approach encompassing recovery and re-use. A novel aspect of the analysis was the inclusion of sanitation systems in India. National phosphorus flows were calculated annually for the five years 2015–2019, and the mean was then used to provide a representative annual flow. The analysis showed that India is dependent on imports for 95% of applied mineral phosphorus fertiliser and has a low phosphorus-use efficiency of 32%. The largest recoverable flow is human excreta (urine and faeces), equivalent to 21% of the current phosphorus applied in mineral fertiliser in India. Phosphorus recovery from septic tanks, the most prevalent sanitation system in India, could alone replace 8% of phosphorus applied in mineral fertiliser in India. Alongside the ongoing development of sanitation systems in India this provides an opportunity to ensure that nutrient recovery is included in sanitation developments.