While food is mainly produced in rural areas, the main drivers of consumption are urban environments. The increasing demand for food in cities leads to an accumulation of phosphorus (P) in urban environments, which affects P flows at multiple scales. This study reviewed recent advances, challenges, and opportunities for sustainable management of P flows in decoupled rural–urban environments. We discussed recent advances in Substance Flow Analysis (SFA) that enable the characterization of P flows in rural–urban environments and illustrate how urban consumption affects rural food production systems. Most challenges of SFA are associated with the (1) spatial decoupling of food production in rural areas and food consumption in urban systems at multiple scales, (2) temporal implications of substance flows on system analysis, and (3) increasing complexity of resource flows in rural–urban environments. We identified three main opportunities for future research on sustainable management of P flows. These opportunities lie in linking urban and rural SFA through multi-scale analysis, increasing both spatial and temporal resolution of P flows within various environments and identifying how linking urban to rural environments can reduce pressure on primary production systems. Also, we highlighted that methodological development on high-resolution SFA at multiple scales is needed to close P cycles between rural and urban systems and to allow the development of future, sustainable P management systems in the anthropogenic food production chain.