Soil minerals influence the biogeochemical cycles of fluoride (F) and phosphorus (P), impacting soil quality and bioavailability to plants. However, the cooperative mechanisms of soil minerals in governing F and P in the soil environment remain a grand challenge. Here, we reveal the essential role of a typical soil mineral, montmorillonite (Mt), in the cycling and fate of F and P. The results show that the enrichment of metal sites on the Mt surface promotes the mineralization of F to the fluorapatite (FAP) phase, thereby remaining stable in the environment, simultaneously promoting P release. This differential behavior leads to a reduction in the level of F pollution and an enhancement of P availability. Moreover, solid-state NMR and HRTEM observations confirm the existence of metastable F−Ca−F intermediates, emphasizing the pivotal role of Mt surface sites in regulating crystallization pathways and crystal growth of FAP. Furthermore, the in situ atomic force microscopy and theoretical calculations reveal molecular fractionation mechanisms and adsorption processes. It is observed that a competitive relationship exists between F and P at the Mt interface, highlighting the thermodynamically advantageous pathway of forming metastable intermediates, thereby governing the activity of F and P in the soil environment at a molecular level. This work paves the way to reveal the important role of clay minerals as a mineralization matrix for soil quality management and offers new strategies for modulating F and P dynamics in soil ecosystems.