The aim of this work was to gain insights into the role of manganese in MnSBA-15 support for gold in the base-free glucose oxidation with H2O2 using a microwave reactor. MnSBA-15 (manganese—acidity source) and SBA-15 (for comparison) were modified with Au (2.2 wt. %) and Cu (for comparison). The physicochemical properties of the catalysts were investigated by XRD, N2 ads/des, TEM, UV-vis, XPS, pyridine adsorption combined with FTIR, ATR-FTIR, and 2-propanol decomposition. The effects of the Mn presence in the support, Au NPs size that determines the number of active Au centers, and the Fermi energy (EF), together with the effects of the pore size, reaction temperature, and time on the activity and selectivity of the applied catalysts were assessed and discussed. It has been demonstrated that the presence of Mn generated Lewis acid centers which did not participate in glucose and H2O2 adsorption, and thus, were not directly involved in the reaction pathway. Both reagents were adsorbed on gold nanoparticles. H2O2 was decomposed to molecular oxygen which oxidized glucose to gluconic acid (50–90% of glucose conversion depending on the reaction time and ~100% selectivity). The presence of manganese in MnSBA-15 was responsible for increased Au NPs size and only slightly influenced the negative charge on gold particles. To achieve effective activity a compromise between the number of active gold species and the level of EF has to be reached (for 5.7 nm Au NPs).