Phosphorus (P) deficiency and fixation are major constraints to crop productivity in tropical soils, yet their large-scale interactions remain poorly understood. This study provides a national-scale assessment of how short-range-ordered iron (Feₒₓ) and aluminum (Alₒₓ) oxides, soil properties, and climate jointly regulate P availability across Nigeria. A total of 1,382 topsoil samples (0–20 cm), collected using a hierarchical Soils4Africa framework, were analyzed for extractable P, Feₒₓ, Alₒₓ, soil organic carbon (SOC), texture, and pH, and integrated with precipitation data. We developed a phosphorus sorption index (PSI) to quantify fixation potential as the molar ratio of oxide abundance to available P. Soil properties varied strongly along agroecological gradients, with Feₒₓ, Alₒₓ, SOC, precipitation, and PSI increasing from semi-arid savannas to humid forest systems, while pH declined. Contrary to the expected inverse relationship, extractable P was positively associated with Feₒₓ, Alₒₓ, SOC, and precipitation, but negatively related to PSI. Multivariate analyses clarified this apparent paradox: SOC exerted the strongest positive effect on P availability, whereas Alₒₓ had a strong negative effect consistent with sorption, and precipitation influenced P both directly and indirectly through oxide accumulation. These results demonstrate that P availability and fixation are not simply inversely coupled but are co-regulated by climatic and biological processes. The PSI effectively captured spatial variation in fixation potential, with the highest values in humid regions characterized by intensive weathering. These findings highlight the dominant role of agroecological gradients in structuring P dynamics and reveal contrasting nutrient constraints across regions: oxide-rich humid soils are limited by fixation, whereas northern savannas are constrained by low inherent P. This study provides a mechanistic basis for site-specific phosphorus management and supports the development of sustainable nutrient strategies to improve P-use efficiency in tropical agroecosystems.