The unique properties of NB, such as its nano-size effect and greater adsorption capacity, have the potential to mitigate ammonia (NH3) emission, but may also pose threats to soil life and their associated processes, which are not well understood. We studied the influence of different NB concentrations on NH3emission, soil microbial biomass, nutrient mineralization, and corn nutrient uptake from farmyard manure (FM). Three different NB concentrations i.e., 12.5 (NB1), 25 (NB2), and 50% (NB3), alone and in a fertilizer mixture with FM, were applied to corn. NB1 alone increased microbial biomass in soil more than control, but other high NB concentrations did not influence these parameters. In fertilizer mixtures, NB2 and NB3 decreased NH3emission by 25% and 38%, respectively, compared with FM alone. Additionally, NB3 significantly decreased microbial biomass carbon, N, and soil potassium by 34%, 36%, and 14%, respectively, compared with FM. This toxicity to soil parameters resulted in a 21% decrease in corn K uptake from FM. Hence, a high NB concentration causes toxicity to soil microbes, nutrient mineralization, and crop nutrient uptake from the FM. Therefore, this concentration-dependent toxicity of NB to soil microbes and their associated processes should be considered before endorsing NB use in agroecosystems.