A series of trimetallic Ni–Mo–W catalysts supported on cubic mesoporous silica (SBA-16) modified with Ti were prepared with the aim to study the effect of Ti incorporation method (sol-gel against pore volume post-synthesis impregnation) on the physical and chemical properties of the synthetized materials. The catalytic behavior of the sulfided catalysts was evaluated in the reaction of hydrodesulfurization (HDS) of dibenzothiophene (DBT). The catalyst characterization by variety of techniques demonstrated that one-pot synthesis led to Ti ions incorporation into SBA-16 structure and an increase of acidity whereas the post-synthesis method led to formation of octahedral Ti species decorating support's surface. The catalytic behavior was closely linked with the characteristics of their oxide precursors. The catalysts prepared by sol-gel method demonstrated to be more effective toward S-removal from DBT than the catalyst modified by post-synthesis method. The initial HDS activity of the best NiMoW/S16–Ti catalyst doubled that of NiMoW/SBA-16 and a commercial NiMo/γ-Al2O3 which was linked with its better textural properties, acidity and adequate active phases dispersion. The main effect of the support modification with Ti was the enhancement of selectivity toward HYD route products. The best hydrogenation selectivity was archived by Ti incorporation via post-synthesis method which was linked to the formation of curved Mo(W)S2 layers having a large amount of “brim” HYD sites.