Two copper-exchanged zeolites, Cu/SSZ-13 and Cu/BEA, were studied as catalysts for the selective reduction of NOx by NH3 (NH3-SCR). Their activities for standard SCR (NOx = NO) and fast SCR (NOx = 50% NO + 50% NO2) were measured before and after sulfur poisoning at 250 °C. The effect of 30 ppm SO2 and a mixture of 24 ppm SO3 + 6 ppm SO2 was evaluated. The repetition of subsequent activity measurements served as regeneration method in SCR conditions. SO2 deactivated Cu/SSZ-13 whereas Cu/BEA was only moderately affected. SO3 led to stronger deactivation of both catalysts than SO2. However, also for this case, the Cu/BEA was significantly less affected than Cu/SSZ-13, even though Cu/BEA contained larger amount of stored sulfur. One possible reason for this could be the large pores of Cu/BEA, where the sulfur species possibly resulted in less sterical hindrance than in the small pore SSZ-13 structure. NH3 temperature-programmed desorption (NH3-TPD) showed no loss of storage sites upon sulfur treatment and subsequent regeneration. Partial activity recovery was observed after a period in SCR conditions at 400 °C and 500 °C. Temperature at 300 °C was insufficient to regenerate the catalysts. Diffuse reflectance infrared Fourier transform spectroscopy (DRIFTS) of NO adsorption suggested that SO2 interacts with the ZCuOH sites on Cu/SSZ-13, causing the strong poisoning.