Phosphorus (P) availability is widely assumed to be limited by the formation of metal (Ca, Fe, or Al) phosphate precipitates that are modulated by soil organic matter (SOM), but the SOM-precipitate interactions remain uncertain because of their environmental complexities. Here, we present a model system by quantifying the in situ nanoscale nucleation kinetics of calcium phosphates (Ca-Ps) on mica in environmentally relevant aqueous solutions by liquid-cell atomic force microscopy. We find that Ca-P precipitate formation is slower when humic acid (HA) concentration is higher. High-resolution transmission electron microscopy observations demonstrate that HA strongly stabilizes amorphous calcium phosphate (ACP), delaying its subsequent transformation to thermodynamically more stable phases. Consistent with the formation of molecular organo-mineral bonding, dynamic force spectroscopy measurements display larger binding energies of organic ligands with certain chemical functionalities on HA to the initially formed ACP than to mica that are responsible for stabilization of ACP through stronger HA-ACP interactions. Our results provide direct evidence for the proposed importance of SOM in inhibiting Ca-P precipitation/transformation. We suggest that similar studies of binding strength in SOM-Fe/Al-P may reveal how both organic matter and metal ions control P availability and fate, and thus the eventual P management for agronomical and environmental sustainability.