Phosphorus is a critical nutrient in sustaining food production. In agricultural systems, application of P fertilizers has significantly increased since the green revolution to become common practice globally, contributing to increased productivity. However, excess use of P fertilizer does not only pose a cost to farmers, but costs for society in the form of water quality problems and environmental degradation. Furthermore, rock phosphates from which these fertilizers are derived are a finite resource, which brings into question the long-term sustainability of this resource and the food production it supports. Soils play a critical role in hosting the P cycle, and organic forms of P (monoesters, diesters) often represent a significant portion of soil P stocks, that are so often overlooked. The mineralization of organic P by phosphatase enzymes is recognized as a key mechanism for converting organic to inorganic forms, which can then be potentially used for P uptake by plants. However, quantification of their contribution still remains a significant challenge. In order to sustainably meet growing food production demands over the next century and reduce the impacts of P fertilizers on waterways, there is a need to understand the extent that soil organic P is available, or can be made available for plants. Here, we present recent findings from a soil-plant biogeochemical model of integrated carbon-nitrogen-phosphorus cycling in agricultural environments. Comparison of observational yield data taken from various long-term experimental sites with model simulations indicate a gap in current scientific understanding of P sources. Whilst yields in the experiments are maintained under low P addition conditions, the model indicates yield declines due to exhaustion of available P resources. We use the model to explore the missing links: potential P inputs, processes and pathways. Finally, we discuss the need for additional empirical evidence to support understanding of organic P cycling, and development of models to include these processes to inform future land management and ensure long-term food security and sustainable water resources.