The objective of our study was to prepare Y-, USY- and ZSM-5-based catalysts by hydrothermal synthesis, followed by copper active-phase deposition by either conventional ion-exchange or ultrasonic irradiation. The resulting materials were characterized by XRD, BET, SEM, TEM, Raman, UV-Vis, monitoring ammonia and nitrogen oxide sorption by FT-IR and Diffuse Reflectance Infrared Fourier Transform Spectroscopy (DRIFTS). XRD data confirmed the purity and structure of the Y/USY or ZSM-5 zeolites. The nitrogen and ammonia sorption results indicated that the materials were highly porous and acidic. The metallic active phase was found in the form of cations in ion-exchanged zeolites and in the form of nanoparticle metal oxides in sonochemically prepared catalysts. The latter showed full activity and high stability in the SCR deNOx reaction. The faujasite-based catalysts were fully active at 200–400 °C, whereas the ZSM-5-based catalysts reached 100% activity at 400–500 °C. Our in situ DRIFTS experiments revealed that Cu–O(NO) and Cu–NH3 were intermediates, also indicating the role of Brønsted sites in the formation of NH4NO3. Furthermore, the results from our experimental in situ spectroscopic studies were compared with DFT models. Overall, our findings suggest two possible mechanisms for the deNOx reaction, depending on the method of catalyst preparation (i.e., conventional ion-exchange vs. ultrasonic irradiation).