The experimental research focused on the influence of solutions containing chicken manure, pig slurry, and silage on the hydration processes of cements and clinker minerals such as C3S, β-C2S, C3A, and C4AF. The results showed that the hydration of C3S and β-C2S led to the formation of various phases, including Ca(OH)2, CaCO3, and various types of poorly crystalline C-S-H phases contaminated with Mg, S, P, Ti, K, and Cl elements. The C3A phase was the most susceptible to biological corrosion, while the C4AF phase was the most resistant. Studies on model cement demonstrated a significant influence of solution pH on bacterial presence, where pH ≥ 9 prevented their occurrence, while pH ≤ 4 and pH 6-7 favored their presence. The addition of γ-C2S and C12A7 phases to the model cement caused a modification of the sample's microstructure and revealed exceptional density, where all spaces were fully occupied by hydration products. Such a model of cement matrix construction prevents and limits the penetration of the corrosive agent into the sample interior. The obtained research results suggest the possibility of using such cement for bioreactor construction and employing additions of calcium aluminates and calcium ferrites to further enhance cement resistance to biological corrosion.