The use of biological agents in biotechnological processes is limited by the strict dependence of their biological activity on environmental conditions: pH, UV radiation, heavy metal salts, temperature, etc. Among the methods of protecting bioagents from negative conditions, the method of encapsulating living cells in a silicon matrix stands out. The cell is surrounded by a porous shell through which an effective exchange of substances between the cell and the environment can take place, but at the same time, the cell is not exposed to aggressive environmental factors. An important component in the sol–gel synthesis of biohybrids are alkylalkoxysilanes, which include tetraethoxysilane, dimethyldiethoxysilane and isobutyltriethoxysilane. The use of alkylalkoxysilanes allows the number of bonds formed between molecules to be varied. Isobutyltriethoxysilane is a substance in which there is a non-hydrolysable bond from an Si atom to a branched isobutyl radical. It is thought that a small amount of it will form a less rigid but stronger shell around microbial cells. In this work, we have characterised functional biomaterials obtained by immobilising microorganisms by means of the sol–gel method using isobutyltriethoxysilane. It is shown that the catalytic activity of the obtained hybrid material is not high, but the use of insignificant amounts of isobutyltriethoxysilane leads to the reliable encapsulation of microorganisms. Therefore, such a material can be used not only in environmental monitoring for the production of biofilters and biosensors, but also in the production of porous materials as carriers of substances.