Functionalized halloysite was used as a support for the immobilization of an enzyme. The surface of halloysite was modified with amino (–NH), epoxy (–C(O)C) and carbonyl (–C=O) groups. Both unmodified and modified forms of the support underwent a comprehensive physicochemical and structural evaluation, including morphological, structural, thermogravimetric and spectroscopic analysis. Aminoacylase from Aspergillus melleus was used as the enzyme in the immobilization process. The process of immobilization by adsorption was performed for 1, 6 and 24 h using different concentrations of enzyme solution (0.5, 1 and 3 mg/cm3). The quantity of aminoacylase loaded onto the support was calculated by the Bradford method. Free and immobilized aminoacylase were used to catalyze the deacetylation of N-acetyl-L-methionine. Additionally, the thermal and chemical stability of the obtained biocatalytic systems were evaluated, as well as the reusability of the immobilized systems. The biocatalytic system with amino groups demonstrated activity above 70% in the pH range 4–9 and 60% in the temperature range 30–70 °C. Aminoacylase immobilized on amino-functionalized halloysite also retains around 50% of its initial activity after five reaction cycles.