Food protein hydrolysates are often produced in unspecific industrial batch processes. The hydrolysates composition underlies process-related fluctuations and therefore the obtained peptide fingerprint and bioactive properties may vary. To overcome this obstacle and enable the production of specific hydrolysates with selected peptides, a ceramic capillary system was developed and characterized for the continuous production of a consistent peptide composition. Therefore, the protease Alcalase was immobilized on the surface of aminosilane modified yttria stabilized zirconia capillaries with a pore size of 1.5 µm. The loading capacity was 0.3 µg enzyme per mg of capillary with a residual enzyme activity of 43%. The enzyme specific peptide fingerprint produced with this proteolytic capillary reactor system correlated with the degree of hydrolysis, which can be controlled over the residence time by adjusting the flow rate. Common food proteins like casein, sunflower and lupin protein isolates were tested for continuous hydrolysis in the developed reactor system. The peptide formation was investigated by high-performance liquid chromatography. Various trends were found for the occurrence of specific peptides. Some are just intermediately occurring, while others cumulate by time. Thus, the developed continuous reactor system enables the production of specific peptides with desired bioactive properties. © 2018, The Author(s).