Based on a long-term field experiment located in Osiny Experimental Station of IUNG-PIB Puławy, microbial characteristic of soil under winter wheat grown in the ecological and conventional systems were compared. The main groups of microorganisms involved in nitrogen and phosphorus transformation processes were analyzed in this work. The obtained results have shown that populations of almost all the tested groups of microorganisms, particularly those of: Azotobacter spp., symbiotic bacteria (rhizobia), ammonifying and nitrifying bacteria, and mycorrhizal fungi (VAM), were higher in the soil under winter wheat grown in the ecological management system contained than in the soil in the conventional system.