Rapid worldwide urbanization calls for a better understanding of phosphorus (P) metabolism and the interaction of the physical, ecological and social drivers of P cycling in urban systems. We quantified the P metabolism in Longyan, a city with a major agricultural economy, and analyzed its long-term trends over the rapid urbanization period of 1985–2010. Both input P (from 4811 t P to 14,296 t P) and output P (from 4565 t P to 13,509 t P) increased significantly. The agricultural subsystem contributed most to the P metabolism, accounting for 85% of total P input. The share of P input lost to the environment, i.e. discharge to water, accumulation in the soil and landfill, increased from 66% to 72%, while food production efficiency decreased from 48% to 29%. Per capita P input showed linear relationships with the Human Development Index (HDI), S-curve relationship with the urbanization rate, and logistic curve relationship with per capita disposable income. A more meat-based diet shift both in Longyan and surrounding cities greatly affected Longyan’s food production structure. Our results demonstrate that P metabolic quantity, configuration, and efficiency in production systems can change drastically in response to changes in consumer and producer behavior as well as in socioeconomic structure. A larger regional scale should be considered in urban P management, when trying to mitigate the increase in P use.