The use of salt- or macro-sized NPK fertilizers is typically associated with low nutrient use efficiency and water eutrophication. Nanotechnology can overcome such drawbacks, but its practical application on a large scale is limited by (i) high costs and difficult scale-up of nanoparticle synthesis, (ii) questionable advantages over traditional methods, and (iii) health hazards related to nanomaterial introduction in the food stream and the environment. Here, we report on a novel biocompatible and multifunctional P nanofertilizer obtained by self-assembling natural or synthetic humic substances and hydroxyapatite nanoparticles using a simple and straightforward dipping process, exploiting the interaction between the polyphenolic groups of humic substances and the surface of nanohydroxyapatite. Pot tests using the as-prepared materials were performed on as a model crop, and the results were compared to those obtained using commercial fused superphosphate and bare nanohydroxyapatites. A significant improvement, in terms of early plant growth, corn productivity, rhizosphere bacteria, and the resistance to NaCl-induced abiotic stresses, was achieved using hydroxyapatite nanoparticles assembled with humic substances. These effects were ascribed to the synergistic co-release of phosphate ions and humic substances, which are two types of plant-beneficial agents for crop nutrition and stimulation, respectively. The release patterns were proven to be tunable with the amount of humic substances adsorbed on the nanoparticles, inducing competition between humic-substance-driven phosphorous dissolution and block of water contact. Such positive effects on plant growth in association with its intrinsic biocompatibility, simple synthesis, and multifunctionality qualify this novel nanofertilizer as a promising material for large-scale use in the agronomic field.