The concepts of physical and chemical transformations occurring in cement concrete under conditions of microbiological deterioration can be used to control the processes of the destruction of cement concretes in order to ensure the required durability and to predict the service life of products. The study of changes in the structural and phase composition of cement stone made of Portland cement grade CEM I 42.5N in the process of fungal deterioration for 6 months when moistened, as well as a sample of a concrete wall exposed to fungal microorganisms for 20 years, was carried out. Diffractograms of the studied cement stone samples contain a large number of pronounced narrow peaks and indicate a highly crystalline structure of phases with the presence of an X-ray amorphous phase of calcium hydrosilicates and tobermorite gel in the cement stone. Changes in the structure of cement stone under the influence of fungi are confirmed by the data of a derivatographic analysis. A decrease in the content of calcium hydrosilicates and ettringite, as well as other crystalline phases in cement stone, leads to a decrease in compressive strength by about 15% over 6 months of fungal degradation. Similar changes after 20 years of exposure to microorganisms suggest deterioration in the strength characteristics of concrete.