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The application of phosphorus (P)-based nanomaterials (NMs) as fertilizers is suggested as a promising approach in agriculture. Simultaneously, for long-term sustainability, green nanosynthesis, including biosynthesis of NMs, is favored. However, the information of fertilizing effects of biogenic P-based NMs in different P-restricting soil conditions is limited. Here, biologically synthesized nanohydroxyapatite (nHAP, platelet-shaped NMs) and nanophosphorus (nP, spherical NMs) were evaluated for their plant growth promotion and uptake in Japonica rice (Taipei 309) using a “fertigation” approach in artificial soils with low-calcareous (LC) and high-calcareous (HC) conditions. Three chemically synthesized variants of nHAPs (spherical, rod-shaped, and needle-shaped NMs) and three bulk materials, rock phosphate, phosphoric acid, and diammonium phosphate, were also used in the study. In LC and HC soils, the rice germination was significantly increased after exposure to the P-based NMs in comparison to the untreated control. The application of nHAPs and nP to rice plants increased the root and shoot lengths, fresh weight, and biomass of plants in all soil types and the content of both P and Ca in the plants as confirmed using X-ray fluorescence. Transmission electron microcopy revealed that the NMs were taken up by the root system, deposited in the leaves, and were localized to different compartments within the cells of the rice plants. In comparison to the bulk P controls, at the same applied concentrations, nHAPs and nP had better fertilizing effects in rice plants. On evaluating the effects of NMs on plant metabolic enzymes, it was found that nHAPs and nP do not cause any stress after their application. Overall, the results from this study provide the first evidence of uptake and localization of biogenic P-based NMs in rice plants and demonstrate their benefits for plant growth in various soil types.