The deposition of mesoporous silica (SiO2) on carbon nanotubes (CNTs) has opened up a wide range of assembling possibilities by exploiting the sidewall of CNTs and organosilane chemistry. The resulting systems may be suitable for applications in catalysis, energy conversion, environmental chemistry, and nanomedicine. However, to promote the condensation of silicon monomers on the nanotube without producing segregated particles, (OR)4−xSiOxx− units must undergo nucleophilic substitution by groups localized on the CNT sidewall during the transesterification reaction. In order to achieve this preferential attachment, we have deposited silica on oxidized carbon nanotubes (single-walled and multiwalled) in a sol–gel process that also involved the use of a soft template (cetyltrimethylammonium bromide, CTAB). In contrast to the simple approach normally used to describe the attachment of inorganic compounds on CNTs, SiO2 nucleation on the tube is a result of nucleophilic attack mainly by hydroxyl radicals, localized in a very complex surface chemical environment, where various oxygenated groups are covalently bonded to the sidewall and carboxylated carbonaceous fragments (CCFs) are adsorbed on the tubes. SiOC covalent bond formation in the SiO2–CNT hybrids was observed even after removal of the CCFs with sodium hydroxide. By adding CTAB, and increasing the temperature, time, and initial amount of the catalyst (NH4OH) in the synthesis, the SiO2 coating morphology could be changed from one of nanoparticles to mesoporous shells. Concomitantly, pore ordering was achieved by increasing the amount of CTAB. Furthermore, preferential attachment on the sidewall results mostly in CNTs with uncapped ends, having sites (carboxylic acids) that can be used for further localized reactions.