Our article describes a study on the influence of mineral and organic fertilisation and three strains of Trichoderma sp. isolated from Polish soils on the count of moulds, including the Fusarium and Alternaria genera, as well as the soil fertility index and the yield of red beets. Apart from that, the aim of the study was to assess the interaction between Trichoderma sp. and plant pathogens. A field experiment was performed on haplic luvisols soil in 11 combinations: a control sample, a variant with a mineral fertiliser, one with manure and eight variants where tomato or onion waste composts were applied. Some of them were inoculated with Trichoderma atroviride (T1) and/or T. harzianum (T2 and T3) isolates. The total count of moulds and the counts of Trichoderma sp., Fusarium sp., and Alternaria sp. in the soil were the most strongly influenced by the addition of mineral fertiliser and manure. On the other hand, the values of the soil fertility index were the highest in the soil enriched with manure, followed by the soil combinations with tomato waste composts. Vegetable waste composts applied to the soil proved to be good carriers of Trichoderma sp. isolates. The study did not prove any antagonistic effect of Trichoderma sp. isolates on the proliferation of Alternaria sp.