Abstract Nanotechnology holds excessive potential for addressing agricultural challenges such as soil deprivation, nutrient deficiencies, low harvests, and nutrient leaching. Nanofertilizers enable more efficient nutrient absorption by plants due to their enlarged surface area, bestowing viable solutions. Urea–hydroxyapatite hybrid (urea–HA hybrid) was successfully synthesized via a coprecipitation approach by doping nanohydroxyapatite with copper and zinc along with urea. The synthesized nanohybrids were analyzed by applying various techniques such as Fourier transform infrared spectroscopy, energy-dispersive spectroscopy (EDS), scanning electron microscopy, and X-ray powder diffraction (XRD). The evidence for the crystalline structure of HA was confirmed by peaks present in XRD analysis at 25.89°, 28.77°, and 32.11°, while urea was validated at 39.29°. The nanosized HA hexagonal nanorods were approximately 16 ± 1.5 nm, with the incorporation of urea, Cu, and Zn. The components of urea–HA hybrid (Ca, P, C, O, and N) were confirmed by EDS analysis with traces of Si. Antibacterial and antifungal activities were investigated against phytopathogenic microbes. The nanohybrid significantly inhibits the growth of Clavibacter michiganensis, Xanthomonas campestris, Macrophomina phaseolina, and Sclerotium rolfsii. A fertilization trial using urea–HA hybrid on Citrus limon has demonstrated a growth of 30 cm within 8 weeks of treatment, accompanied by brighter-colored leaves. Thus, the synthesized urea–HA hybrid enabled the slow release of nutrients, which had a significant impact on plant growth and will also effectively manage disease control against phytopathogens. Thus, this innovative approach addresses agricultural challenges regarding nutrient delivery and disease control more effectively.