Mesoporous silicas of MCM-41 and MCM-48 types were synthesized and modified with copper by template ion-exchange (TIE) technique. A high dispersion of deposited copper species was managed by subsequent treatment of the samples with ammonia, urea, or acetonitrile solution. Copper-modified silicas were analysed in terms of their chemical composition (ICP-OES), ordering of porous structure (XRD), textural parameters (low-temperature N2 sorption), dispersion and form of introduced copper species (UV–vis-DR, XRD, H2-TPR, NH3-TPD). Mesoporous silicas modified with copper exhibited promising catalytic efficiency in selective catalytic reduction of NO with ammonia (NH3-SCR). The samples containing dispersed copper species (predominantly monomeric copper cations) presented enhanced catalytic activity compared to catalysts containing CuO aggregates. On the other hand, CuO aggregates showed greater catalytic activity in the side process of direct ammonia oxidation by oxygen present in the reaction mixture. It was demonstrated that TIE post-treatment of the samples with urea resulted in most effective improving dispersion of deposited copper and is less destructive for ordered porous structures of mesoporous silica comparing to treatment with ammonia solution.Graphical abstract