Oxide material of a new type, ZrO2·SiO2 (raw and carbonyl-grafted), was used as support in the immobilization of aminoacylase from Aspergillus melleus. The ZrO2·SiO2 was synthesized via sol–gel method. The obtained material was additionally modified with glutaraldehyde. Various physicochemical analyses were used to confirm the effectiveness of the modification and immobilization processes, including Fourier transform infrared spectroscopy, laser Doppler velocimetry and low-temperature N2 sorption. The immobilization process was performed within 3 h using different concentrations of enzyme solution (1, 3, 5 and 7 mg/mL), and the Bradford method was used to determine the quantity of immobilized enzyme. The resulting biocatalytic systems were then used as catalysts in the hydrolysis of different N-acetyl-dl-amino acids (leading to l-methionine, l-cysteine, l-serine and l-tryptophan). Based on this reaction the apparent and relative catalytic activities were determined. The highest activity of the immobilized enzyme was attained in the synthesis of l-methionine (the apparent activities of aminoacylase immobilized on raw and carbonyl-grafted ZrO2·SiO2 were 4112 and 4947 U/g, respectively). Furthermore, the effect of pH and temperature on catalytic activity, as well as the storage stability and reusability of the prepared biocatalytic systems were determined. Aminoacylase immobilized on carbonyl-grafted ZrO2·SiO2 retains 85% of its initial activity after 30 days of storage and 70% after five reaction cycles.