New heterogeneous catalysts were obtained by modification of MWW zeolites (MCM-22 and MCM-56) by swelling and pillaring with niobiosilicate, achieved by two different methods. The main differences between these methods were time and temperature at which the modification was carried out, the concentration of a base used during the modification, and the water content in the catalysts used for further modification. The XRD analysis proved that both methods used gave MCM-36 structure, in all cases pillaring led to an increase in surface area, but some differences in final materials were noted, depending on the pillaring procedure. Both NbMCM-36 zeolites exhibited different content of micropores (lower in the zeolites synthesized from MCM-22), different loading with niobium species (higher in the material prepared from MCM-56) and similar acidity strength. Both niobium containing zeolites were active catalysts in liquid phase cyclohexene oxidation with H2O2 and were successfully used in the second run. Niobium played a role of H2O2 activator. Texture parameters and content of niobium was crucial for the effective discoloration of methylene blue with the use of hydrogen peroxide.