In order to limit losses in mushroom cultivation, various methods and measures are used to prevent the development of pathogens. However, frequently occurs the effective disinfection does not result directly a positive response in the form of increased yielding or at least reduction of the problems of infections with green mould or bubble diseases. The studies presented in this paper show that even with a relatively high level of inoculation of phase II compost containing Trichoderma aggressivum (105/cm3), significantly exceeding the potential intensity of natural infections, Agaricus bisporus remained dominant in the environment. On the other hand, an excessive disinfection disturbed this balance in favor of the more disinfectant-resistant pathogen. High efficacy of the innovative gas ClO2 disinfection, at the applied balance concentration 1000 ppm (m/m) was determined on the surfaces of the cultivation hall. However, the study demonstrates that effective disinfection of compost may give the effects of weakening of mushroom spawn mycelium and domination of its environment by the competing pathogens.