To supply adequate food, the ongoing and unrestrained administration of nitrogen fertilizer to agricultural fields is polluting the climate and living organisms. On the other hand, the agriculture sector urgently needs a technological upgrade to effectively confront hunger and poverty. Here, we report a rapid synthesis of zinc and magnesium-doped hydroxyapatite-urea nanohybrids for slow release and delivery of nitrogen to wheat and rice crops. Nanohybrids slowly release nitrogen for up to six weeks compared to the burst release of nitrogen from urea, and their use substantially reduces, by at least 3.8 times, ammonia emissions into the environment compared with that of urea fertilizer. A half‑nitrogen dose applied as multi-nutrient complexed nanohybrids maintained crop growth, yield, and nutritional compositions in wheat and subsequent rice crops. Nanohybrids enhanced the wheat crop yield and nitrogen uptake by 22.13% and 58.30%, respectively. The synthesized nitrogen nanohybrids remained in the soil for two continuous crop cycles, reduced ammonia volatilization, and achieved nitrogen delivery to the crops. Additionally, soil dehydrogenase activity (534.55% above control) and urease activities (81.82% above control) suggest that nanohybrids exhibited no adverse impact on soil microorganisms. Our comprehensive study demonstrates the advantages of 'doping' as a method for tailoring hydroxyapatite nanoparticles properties for extended agricultural and environmental applications. The use of nanohybrids substantially reduced greenhouse gas emissions and enabled the reduction, by half, of nitrogen inputs into the agricultural fields. This study, therefore, reports a novel nano-enabled platform of engineered hydroxyapatite-urea nanohybrids as a nitrogen fertilizer for efficient nitrogen delivery that results in improved crop growth while minimizing environmental pollution.