Various nanotechnology advancements are used to protect crops and the safety concerns of nanopesticides for soil quality need to be addressed. Soil enzymes and certain beneficial bacteria play a vital role in preserving soil health by carrying out required biochemical reactions. In the present study, clotrimazole, econazole nitrate, and miconazole nitrate based nano-fungicides were investigated for their antifungal efficacy followed by their biosafety assessment. Antifungal studies of all the test nano-fungicides demonstrated their effectiveness against Rhizoctonia solani. The relative lesion heights were 29–38% under field conditions and they ranged from 17% to 33% in pot experiments. Impact of these nano-fungicides on urease activity in soil was comparable with the conventional fungicide hexaconazole, as evident from the presence of 0.5–2.7 mg/kg urea-nitrogen after 24 h of 200 mg/kg urea-nitrogen application. In all the treatments, the activity of soil nitrifiers was not adversely affected after application of these nano-fungicides. After 21 days of incubation, the nitrate-N contents were in the range of 150–180 mg/kg in nano-fungicide treated soils as compared to 180 mg/kg of nitrate-N in urea control. Virtual risk assessment using docking of these imidazole derivatives on soil enzymes revealed their behavior similar to that of hexaconazole.