The immobilization of serine protease subtilisin Carlsberg on/in chitosan, a hydrophilic biopolymer was investigated in this study. Using different techniques, biocatalysts in the form of gels, fibers and films were prepared. Subtilisin loading and biocatalytic properties of obtained samples were studied. The optimal method of enzyme incorporation was pre-mixing of chitosan acetate and enzyme solutions, then air-drying and treatment with glutaraldehyde. It was found that this form of biocomposite has the highest loading capacity (up to 20 mg protein g−1 support) and good mechanical properties. The dependence of subtilisin loading on the starting concentration of the enzyme during immobilization shows the maximum loading at [E] = 15 mg mL−1. The dependence of subtilisin loading and activity on the concentration of the glutaraldehyde was explored. The biocatalytic films were active catalysts for peptide bond formation (with 25–92% product yield) in nonaqueous media, demonstrating high activity and stability under these conditions. They are also active in aqueous media, bringing about the reverse reaction, and can therefore be used for either peptide bond formation or cleavage.