The catalytic performance of Fe-catalysts in selective catalytic reduction of nitrogen oxides with ammonia (NH3-SCR) strongly depends on the nature of iron sites. Therefore, we aimed to prepare and investigate the catalytic potential of Fe-MCM-22 with various Si/Fe molar ratios in NH3-SCR. The samples were prepared by the one-pot synthesis method to provide high dispersion of iron and reduce the number of synthesis steps. We have found that the sample with the lowest concentration of Fe exhibited the highest catalytic activity of ca. 100% at 175 °C, due to the abundance of well-dispersed isolated iron species. The decrease of Si/Fe limited the formation of microporous structure and resulted in partial amorphization, formation of iron oxide clusters, and emission of N2O during the catalytic reaction. However, an optimal concentration of FexOy oligomers contributed to the decomposition of nitrous oxide within 250–400 °C. Moreover, the acidic character of the catalysts was not a key factor determining the high conversion of NO. Additionally, we conducted NH3-SCR catalytic tests over the samples after poisoning with sulfur dioxide (SO2). We observed that SO2 affected the catalytic performance mainly in the low-temperature region, due to the deposition of thermally unstable ammonium sulfates.