Phosphorus (P) is both an essential resource, required for plant growth and food production, and a costly pollutant, capable of causing eutrophication in water courses. The possibility of future phosphorus scarcity and the requirement to improve the quality of UK waters necessitates the development of a UK phosphorus management system, which increases use efficiency, reduces losses and recycles wastes more effectively. A vital first step towards creating such a system is to conduct a substance flow analysis (SFA), which maps and quantifies the relevant stocks and flows, allowing specific measures to be implemented that target identified losses and areas of inefficient resource use. This paper presents the results of a SFA for phosphorus in the UK, focussing in particular on the food production and consumption system for the year 2009. The SFA results suggest that the UK population consumed around 31.0 kt P in 2009, which was largely achieved by importing food, feed and fertilisers, with net imports totalling 113.5 kt P. Imported fertilisers accounted for 56% of the total imports, containing 77.5 kt P. The largest losses within the systems were those to water, estimated at around 41.5 kt P/yr, and soil accumulations are estimated at 37.5 kt P/yr. The efficiency of UK crop production is estimated at 81%, whereas the efficiency of producing animal products is only 16.5%. Wastewater treatment works (WwTW) received around 55.0 kt P within wastewater, with 57% being removed in sewage sludge. The 23.5 kt P discharged within final effluent represented the largest loss to UK waters. Around 71% of the sludge was recycled to land, containing 22.5 kt P, although the rate of application was around 5× higher than the uptake rate for crops, demonstrating the challenges of effectively recycling bulky wastes. Existing measures aimed at tackling water pollution and climate change have acted to improve P management in the UK, although additional measures focussing particularly on P as a resource are required. The results from this analysis suggest focussing on P removal and recovery at WwTW, as well as developing more effective methods for recycling bulky wastes such as animal manure, food waste and sewage sludge in order to reduce soil accumulations and replace imported fertilisers. Conducting additional SFAs at smaller scales may be necessary in order to develop more specific measures, such as regional recycling strategies.