Antifungal azole drugs like fluconazole, itaconazole and ketoconazole are widely used for treatment of fungal related diseases including aspergillosis and mucormycosis. This study aimed at biosynthesis of fluconazole, itaconazole and ketoconazole containing oil/water (O/W) nanoemulsions (NE) using Eucalyptus essential oil and its effect against aspergillosis and mucormycosis. Nanoemulsions were synthesized having eucalyptus essential oil, surfactants: tween 80, and co-surfactant: ethanol. Zeta potential, pH, conductivity and droplet size of nano-formulations were studied by using Zeta sizer. Nanoemulsions were analyzed by UV–VIS, FT-IR and fluorescent techniques. Stability studies were conducted by storing the nanoemulsions at different conditions for 60 days. Anti-aspergillosis, anti-mucormycosis and drug release pharmokinetics were evaluated. Average size of nanoemulsions ranged from 245 to 415 nm along with zeta potential from − 9.20 to − 25.4 mV. Encapsulation efficiency of drug loaded nanoemulsions was ranged from 40 to 50%. Nano-droplets displayed stability after 60 days of storage. Considerable anti-aspergillosis and anti-mucormycosis activities were detected. Among all formulations, F1NEs depicted high antifungal activity against Aspergillus strains MTCC 277, MTCC 343 as observed by zone of inhibition (ZOI) values. Against Mucor spp strain MTCC 3373, visual pictures clearly showed substantial inhibition in fungal growth. Pharmokinetic study shown that all nanoformulations showed Korsmeyer–Peppas model.