The biodegradation of building materials refers to the problem of loss of performance due to biological agents, mainly dry rot fungi, moulds (filamentous fungi), bacteria and insects. Biocorrosion not only leads to the damage and deterioration of building materials, but can also pose a direct threat to human health. Inorganic building materials are a difficult substrate for microorganisms because they need food sources for their metabolism. However, they become colonised by microorganisms. In this paper, the effect of mould fungi on the moisture content and structure of CEM I and CEM I cement–polymer mortars with a 5% polysiloxane latex admixture was analysed. The analysis was carried out after 15 months of exposure to the biological environment. It was found that the cementitious materials were susceptible to the corrosive environment in the form of the filamentous fungi Penicillium chrysogenum and Cladosporium herbarum. It was also found that, after 15 months of exposure to mould fungi, CEM I cementitious materials without admixtures were slightly less susceptible to mould fungi than CEM I with the addition of a 5% polysiloxane admixture.