Cover crops are used in the cultivation of various plants. They properly modify the composition of soil microorganisms and can protect of plants from phytopathogens. The purpose of the field and laboratory studies was to determine the quantitative and qualitative composition of microorganisms in the soil under carrot cultivated with the use of oats, tansy phacelia and spring vetch as cover crops. The paper presents also studies on soil-borne fungi threatening the healthiness of carrot roots. In the conventional cultivation of carrot the population of bacteria (including Pseudomonas spp. and Bacillus spp.) was the smallest, while after the application of oats it was the largest. Oats and spring vetch were most effective in limiting the occurrence of soil-borne fungi. Those plants and tansy phacelia caused an increase of the population of saprotrophic fungi (Albifimbria spp., Clonostachys spp. and Trichoderma spp.) in the soil. Intercrop plants had a positive effect on the healthiness of carrot seedlings and roots. Alternaria dauci, A. alternata, A. radicina, Fusarium oxysporum, Globisporangium irregulare, Neocosmospora solani, Phytophthora sp., Rhizoctonia solani and Sclerotinia sclerotiorum proved to be the most harmful towards the studied underground parts of carrot. Oats proved to be the most effective in inhibiting the occurrence of the pathogenic fungi for Daucus carota L.