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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 viaa 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 limonhas 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.

•Four potato cultivars (Ronoldo, Rubi, Challenge, and Sadaf) demonstrated robust resistance against the highly destructive Black Scurf disease, caused by Rhizoctonia solani.•The incidence of the disease displays a strong negative correlation with key physiological parameters, including chlorophyll levels, protein content, and enzyme activities, underscoring the detrimental impact of the disease on the overall health of potato plants.•Notably, enzymes such as catalase, peroxidase, and polyphenol oxidase exhibit significant alterations in their activity levels in response to the disease, signifying their potential utility as reliable indicators for identifying and characterizing resistant potato cultivars.