The aim of the study was to assess the influence of organic and natural fertilisation under maize plantation grown in monoculture on the number of selected groups of microorganisms. The experiment was conducted between 2005 and 2007 in plots of the Experimental and Educational Station in Swadzim, Department of Agronomy, Poznań University of Life Sciences, Poland. Soil taken from maize for silage was the research material. Soil samples for microbiological analyses were collected at a particular phase of maize development: before sowing; at the phase of maize emergence (BBCH 11-13); at the phase of 3-4 maize leaves (BBCH 13-14), at the phase of 6-7 maize leaves (BBCH 16-17), at the phase of panicle florescence (BBCH 63-69), at the phase of wax maturity (BBCH 87-89). The number of selected groups of microorganisms in the soil samples (moulds, total bacterial count, proteolytic and ammonifying bacteria, copiotrophs, oligotrophs and actinobacteria) was measured with the pour plate method developed by Koch. Between 2005 and 2007 natural and organic fertilisation in plots with a maize monoculture grown for silage increased the intensity of proliferation in all the groups of microorganisms under study. The trend and rate of variation in the microorganisms depended on the type of organic matter applied to soil and the term of analyses related with the plants’ stage of development.