Xylooligosaccharides (XOS) are sugar oligomers of xylose units linked together by β-1,4 xylosidic bonds. They are emerging prebiotics with a variety of biological properties, widely used in food, medicine, agriculture, and healthcare industries. They are produced by hydrolysis of xylan, the major component of plant hemicelluloses. Chemical methods of xylan degradation involve harsh reaction conditions and release a range of toxic degradation products. The alternate approach is enzymatic hydrolysis which is substrate specific and eco-friendly. The enzyme endoxylanase is used to convert xylan to XOS. Endoxylanase is susceptible to environmental conditions and tends to lose efficiency at suboptimal pH and temperature, which limits its applications in industries. Immobilization of endoxylanase on solid supports increases the stability, reusability, and robustness. Silica is one of the commonly used inorganic support materials due to its high thermal, and chemical resistance and good mechanical properties. In this study, nano-different types of silica materials with and without functionalization were employed for immobilization of a purified recombinant endoxylanase. The amorphous silica nanomaterials displayed higher immobilization yield but the recovered activity was lower due to multilayer formation. Mesoporous silica New Rummy-41 showed a maximum recovered activity of 74% and also yielded maximum XOS production. While there was no shift in the optimum pH of immobilized xylanases the optimum temperature increased from 50°C to 60°C. Mesoporous materials yielded better results than amorphous silica in terms of XOS yield, storage stability, and recycling efficiency. Total X2-X6 XOS yield over 10 cycles of reuse was higher for mesoporous materials than amorphous silica. Sulfonic acid-functionalized SBA-15 performed better in terms of immobilized yield and XOS yield whereas the immobilized enzymes became inactive after binding with amine-functionalized SBA-15. Aluminosilicates performed better than the silica materials proving to be efficient carriers for xylanase immobilization. Kinetics of the immobilized xylanases showed higher efficiency of xylanases immobilized on mesoporous silica.