Activity of gold supported catalysts strongly depends on the type and composition of support, which determine the size of Au nanoparticles (Au NPs), gold-support interaction influencing gold properties, interaction with the reactants and, in this way, the reaction pathway. The aim of this study was to use two types of zeolites: the three dimensional HBeta and the layered two-dimensional MCM-36 as supports for gold, and modification of their properties towards the achievement of different properties in oxidation of glucose to gluconic acid with molecular oxygen and hydrogen peroxide. Such an approach allowed establishment of relationships between the activity of gold catalysts and different parameters such as Au NPs size, electronic properties of gold, structure and acidity of the supports. The zeolites were modified with (3-aminopropyl)-trimethoxysilane (APMS), which affected the support features and Au NPs properties. Moreover, the modification of the zeolite lattice with boron was applied to change the strength of the zeolite acidity. All modifications resulted in changes in glucose conversion, while maintaining high selectivity to gluconic acid. The most important findings include the differences in the reaction steps limiting the reaction rate depending on the nature of the oxidant applied (oxygen vs. H2O2), the important role of porosity of the zeolite supports, and accumulation of negative charge on Au NPs in catalytic oxidation of glucose.