The conversion of biomass components catalyzed via immobilized enzymes is a promising way of obtaining valuable compounds with high efficiency under mild conditions. However, simultaneous transformation of glucose and xylose into gluconic acid and xylonic acid, respectively, is an overlooked research area. Therefore, in this work we have undertaken a study focused on the co-immobilization of glucose dehydrogenase (GDH, EC 1.1.1.118) and xylose dehydrogenase (XDH, EC 1.1.1.175) using mesoporous Santa Barbara Amorphous silica (SBA 15) for the simultaneous production of gluconic acid and xylonic acid. The effective co-immobilization of enzymes onto the surface and into the pores of the silica support was confirmed. A GDH:XDH ratio equal to 1:5 was the most suitable for the conversion of xylose and glucose, as the reaction yield reached over 90% for both monosaccharides after 45 min of the process. Upon co-immobilization, reaction yields exceeding 80% were noticed over wide pH (7–9) and temperature (40–60 °C) ranges. Additionally, the co-immobilized GDH and XDH exhibited a significant enhancement of their thermal, chemical and storage stability. Furthermore, the co-immobilized enzymes are characterized by good reusability, as they facilitated the reaction yields by over 80%, even after 5 consecutive reaction steps.