Phosphorus (P) is an essential fertilizer for agricultural production but is also a potent aquatic pollutant. Current P management fails to adequately address both the issue of food security due to P scarcity and P pollution threats to water bodies. As centers of food consumption and waste production, cities transport and store much P and thus provide important opportunities to improve P management. Substance flow analysis (SFA) is often used to understand urban P cycling and to identify inefficiencies that may be improved on. However, SFAs typically do not examine the factors that drive observed P dynamics. Understanding the social, ecological, and technological context of P stocks and flows is necessary to link urban P management to existing urban priorities and to select local management options that minimize tradeoffs and maximize synergies across priorities. Here, we review P SFA studies in 18 cities, focusing on gaps in the knowledge required to implement P management solutions. We develop a framework to systemically explore the full suite of factors that drive P dynamics in urban systems. By using this framework, scientists and managers can build a better understanding of the drivers of P cycling and improve our ability to address unsustainable P use and waste.