Mesoporous silica materials of MCM-48 and MCM-41 types were synthetized by surfactant directed methods and modified with copper by template ion-exchange (TIE) protocol and its extended version including post-treatment of modified silicas with ammonia solution. Obtained samples were characterized with respect to their textural parameters (low-temperature N2 sorption), porous structure, chemical composition, surface acidity (NH3-TPD), form and aggregation of deposited copper species (UV–vis-DRS) as well as their reducibility (H2-TPR). It was shown that application of TIE method resulted in deposition of copper into MCM-48 in more dispersed forms comparing to MCM-41. Both, in the case of MCM-41 and MCM-48, treatment of the samples with ammonia directly after copper introduction resulted in deposition mainly monomeric copper cations. The catalysts containing such dispersed copper species were more active in the low-temperature NH3-SCR process. The NO conversion above 90% with selectivity to N2 above 97% was obtained in the temperature range of 225–325 °C. CuO aggregates, deposited on mesoporous silicas, were found to be active in the side process of direct ammonia oxidation at higher temperatures.