An enzymatic monolith microreactor was used for the first time in the continuous hydrolysis of hemicelluloses to obtain xylo-oligosaccharides with nutraceutical properties. For this purpose, Thermomyces lanuginosus xylanase was entrapped into hybrid sol-gel matrices formed by diverse alkoxysilanes. The structural characteristics of these biocatalysts were extensively investigated by FTIR to assess the enzyme secondary structure modification during the entrapment procedure. Their catalytic performances were evaluated in both batch and continuous experiments. For batch experiments, xylo-oligosaccharides were produced with a yield of 30%, as xylose equivalent amount, from 1% (w/v) xylan from birchwood. Furthermore, after a 96 h of recycle experiment, 70.6% of residual xylanase activity was recorded. For the xylan saccharifications in continuous microreactors, 18% of equivalent xylose was constantly produced for 39 h, from a xylan solution of 0.25 mg/ml. The obtained products suggested that a modulation towards specific xylo-oligosaccharides can be performed by a suitable choice of the entrapment system.