Co-containing HAlBEA zeolite was obtained by conventional wet impregnation of HAlBEA zeolite with an aqueous Co(NO3)2.6 H2O solution, whereas Co-containing SiBEA zeolites were prepared by a two-step post-synthesis method. This approach consists of, in the first step, dealumination of parent BEA zeolite to obtain an aluminium-free SiBEA support and then, in the subsequent step, contact of the obtained material with an aqueous solution of cobalt nitrate. As shown by X-ray diffraction and low-temperature N2 adsorption, the dealumination of BEA zeolite and introduction of cobalt ions did not involve destruction of zeolite structure, and only insignificant blocking of pore system was observed after introduction of high amounts of cobalt. Nevertheless, clear changes in acidity were found by FTIR of pre-adsorbed pyridine after dealumination of parent BEA zeolite and introduction of cobalt ions. The presence of Lewis acid sites resulted in enhanced selectivity to CO and benzene formed as by-products in the toluene combustion. Therefore, SiBEA zeolite was chosen as a support for an introduction of various amounts of Co into the zeolite structure (the intended Co contents of 3.0–9.0 wt%). Depended on the amount of the introduced Co, cobalt was incorporated into the framework of BEA zeolite as isolated mononuclear Co(II) species, small Co(II) oxide clusters and/or Co3O4 crystallites distributed in the whole zeolite structure. The chemical environment and dispersion of cobalt species were studied by transmission electron microscopy (TEM), FTIR of pre-adsorbed NO, UV–vis diffuse reflectance spectroscopy and X-ray photoelectron spectroscopy (XPS). Temperature-programmed reduction of hydrogen (H2-TPR) was also performed to determine reducibility of the Co-containing SiBEA zeolites. It was confirmed that siliceous SiBEA zeolite was the excellent support of Co3O4, which was in turn recognized as the main active phase in the total oxidation of toluene. The best catalytic performance was achieved over the catalysts containing at least 0.05 mmol of Co in the form of Co3O4 per 1 g of SiBEA zeolite.