Our study presents the results of field experiments whose aim was to assess the development of the root system of maize cultivars with different genetic profiles, depending on the method of soil preparation for sowing and NP fertilizer application. Laboratory tests included an assessment of the effect of mineral fertilizers used in field trials on selected groups of microorganisms that occur (or could potentially occur) in the soil environment. The “stay-green” cultivar was characterized by significantly higher indicators of soil overgrowth with roots in the 0-15 cm and 15-30 cm soil profiles than the classical cultivar. Row application of NP fertilizer stimulated the development of a maize root system in a 0-15 cm soil profile. The “stay-green” cultivar showed a positive reaction of root system development to row NP application. Model studies showed significant relationships associated with the chemical composition of mineral fertilizer or its dose and growth inhibition growth of microorganisms that could be part of the soil ecosystem.