Nanoscale hydroxyapatite (nHA) was synthesized to investigate its potential as a phosphorus (P) ensembled nanofertilizer, using soybean (Glycine max L.) as a model plant. The conventional analogue phosphate (pi) was used for comparison with the synthesized nHA. Varied precipitation intensities (0%, 30%, 60%, and 100%) were simulated by adding selected volumes of the P fertilizers (nHA or pi) via foliar spray and soil amendment. The total amounts of added P were the same across all the treatments. The importance of a wash-off effect was investigated on foliar-treated seedlings by evaluating different watering heights (20, 120, and 240 cm above the seedlings). Fresh weight, pigment content, macro-, and micronutrient contents were measured in soybean tissues across all the treatments after 4 weeks of greenhouse cultivation. The synthesized nHA showed superior effects on plant nutrient content upon high precipitation intensities. For example, at 100% precipitation intensity, there was 32.6% more P and 33.2% more Ca in shoots, 40.6% more P and 45.4% more Ca in roots, and 37.9% more P and 82.3% more Ca in pods, as compared to those with pi treatment, respectively. No impact on soybean biomass was evident upon the application of nHA or pi. Further investigation into customizing nHA to enhance its affinity with crop leaves and to extend retention time on the leaf surface is warranted given that the present study did not show significant positive impacts of nHA on soybean growth under the effects of precipitation. Taken together, our findings increase understanding of the potential application of nHA as a nano-enabled fertilizer in sustainable agriculture.