Purely siliceous and niobium-containing mesoporous molecular foams (MCFs) were synthesized by modifying a standard synthesis route. This was accomplished by decreasing considerably the content of chloride ions in the gel. The samples prepared under such conditions contained the MCF and SBA-15 phases. Mesostructured cellular foams were modified with (3-mercaptopropyl)trimethoxysilane (MPTMS) and (3-aminopropyl)trimethoxysilane (APTMS) via the direct synthesis, with increased efficiency of formation of the spherical MCF phases. All the materials obtained were characterized by XRD, sorption of nitrogen, FT-IR, UV–Vis, thermogravimetric analysis, 29Si MAS NMR, 13C CP/MAS NMR, and electron microscopy. We demonstrated that organosilanes added at the end of the synthesis procedure play a double role; as a source of the anchored catalytic active species (propylamines and propylsulfonic chains) and a source of methanol released during the interaction between MPTMS (APTMS) and hydrolyzed tetraethyl orthosilicate (TEOS). The methanol obtained in this way acts as a co-surfactant increasing the activity of ethanol released during hydrolysis of TEOS and enhancing the transformation of cylindrical SBA-15 towards the spherical MCF phase. Finally, it was shown that niobium species enhanced the oxidation of thiol groups in MPTMS towards sulfonic species and also affected slightly the morphology of the samples. The presence of niobium moieties did not influence, however, the formation of the pure MCFs mesostructured materials and their structural parameters.