Phosphorus (P) is an essential element for life on Earth, with an important and oftentimes unaccounted organic biogeochemical component. Current methods for the quantification of different organic P compounds in environmental samples (e.g., soils, sediments) are based on extraction techniques and often associated with incomplete P recovery or sample changes. In this study, we present a protocol for the quantification of different organic and inorganic P species in soils using synchrotron-based X-ray absorption near-edge structure (XANES) spectroscopy at the P L2,3-edge. Its accuracy and precision was evaluated by analyzing 40 standard mixtures composed of seven different inorganic and organic P compounds (with a mean of R2 = 0.85). In addition, we quantified the P species of two soils and two agro-industrial byproducts using P L2,3-edge XANES spectroscopy and the results were compared with those obtained by P K-edge XANES or 31P NMR spectroscopy. Using the P L2,3-edge, we identified different organic P species, including those not identified by the common P K-edge XANES. However, there is a consistent underestimation of organic polyphosphates. Overall, the application of P L2,3-edge XANES provides a higher level of information than by P K-edge XANES, although the ubiquitous use of this novel methodology is still limited to samples with a phosphorus content above 3 mg g-1.