The growth of the nanoproduct market results in the abundance of engineered nanoparticles (ENPs) in the environment, including soils. The very important step regarding to the presence of ENPs in the soil is the evaluation of ENPs effect on the soil microbial community. In the presented study the impact of nano-CuO and nano-ZnO (at 10 mg kg−1) on dehydrogenase activity, the numbers of fungi and of oligo and copiotrophic bacteria was investigated at the 1, 90, 730 days after application of ENPs to soils. The concentrations of water-soluble and CHCl3-labile Cu and Zn in the soil samples were also determined. In most cases, the dehydrogenase activity and the number of bacteria and fungi was different in treated and untreated soil, especially after 1 and 90 days of incubation. The effects of ENPs on the soil microbial community could be related to the different concentration of metals in water soluble fraction. The decrease of Zn and Cu concentrations did not always mean a reduction of the effect of ENPs on the microbial community, which could have been related with the different species composition of the microorganisms and their tolerance and capability of adaptation to the presence of ENPs. We also observed that a long-term exposure of the soil microflora to investigated ENPs did not cause any significant changes in the enzymatic activity and in the size of population of the tested group of microorganisms. Similarly to microbiological indicators, the level of water soluble metal concentration in treated and untreated soil did not differ after 730 days.