Anthropogenic increases in atmospheric CO2 concentration and the connected deposition of organic matter into the soil influence the occurrence of decomposers who regulate carbon release back into the atmosphere. The effects of increased concentration of atmospheric carbon dioxide, plant species cover quality and nitrogen (N) fertilization on the coenosis composition of soil saprobic microfungi were studied under field conditions (Swiss Free Air Carbon Dioxide Enrichment experiment). In total, 42 species of microfungi were detected in examined soil. The most significant response of soil mycoflora was induced by the species identity of plant cover. Higher N fertilization significantly suppressed the abundance of soil microfungi at ambient CO2. The effect of increased CO2 on colony-forming units was not significant when taken as an independent treatment; however, this factor interacted significantly with N availability. Some species, e.g. the Clonostachys rosea, were proven associated with the plant cover components, in this particular case with Trifolium repens. Therefore, we suggest the identity of plant species constituting plant cover as the most important factors affecting soil microfungi in agroecosystems.