An in situ DRIFT investigation of the behavior of iron-molybdenum oxides encapsulated in Boralite (FeMo/Bor) during the oxidation of toluene is reported. The study was carried out to obtain a better understanding of the differences between this catalytic material and (i) V-TiO2 based catalysts and (ii) bulk Fe-2(MoO4)(3). V-TiO2 based catalysts show a severe decrease in the selectivity to benzaldehyde with increasing conversion of toluene, in contrast FeMo/Bor samples. The effect was attributed to the presence of stronger Lewis acid sites in vanadium-based catalysts which, activating the carbon atom of the carbonyl groups, facilitate its nucleophilic attack to form benzoate species which further degrade to carbon oxides. FeMo/Bor shows higher selectivity at low conversion than bulk Fe-2(MoO4)(3), probably due to the presence of nanosized iron-molybdate particles inside the zeolite channels, and lower selectivity at high conversion. Due to back-diffusion limitations inside the zeolite pores, the aromatic ring of the alkylaromatic is oxidatively attacked to form maleic anhydride, precursor of the further oxidation to carbon oxides. In FeMo/Bor a different main pathway is responsible for the lowering of selectivity at high conversion with respect to V-TiO2 based catalysts.