Mycorrhizal fungi influence the development and activity of communities of soil microorganisms. The purpose of this study was to estimate the effect of arbuscular mycorrhizal fungus Claroideoglomus etunicatum (W. N. Becker & Gerd.) C. Walker & Schüβler on the population structure of fungal colonies in the rhizosphere of tomatoes grown in a plastic tunnel. The field experiment was conducted from 2015 to 2017 at an ecological farm in Grądy, central eastern Poland. The object of study were the three tomato cultivars: ‘Antalya F1’, ‘Esmira F1’, and ‘Pelikan F1’. Tomato seedlings were inoculated with C. etunicatum; spores were introduced about 5 cm deep in the rhizosphere of the studied plants (25–30 spores of C. etunicatum for each plant). Each year, mycological analysis of the tomato rhizosphere was conducted using Warcup’s method; structure of fungal communities of the tomato rhizosphere varied depending on the AMF applied. Saprotrophic fungi such as Trichoderma ssp., Mucor spp., and Penicillium spp. were often more isolated from the rhizosphere of plants inoculated with C. etunicatum than that of the control samples. It can be concluded that AMF directly impacted the development of fungal biodiversity in the tomato rhizosphere, particularly regarding the number of saprotrophs in the soil.