In this project, KIT-5 was effectively functionalized with sulfonic groups by grafting and using the co-condensation method and a heterogeneous solid acid catalyst. A co-condensation procedure leading to the stable, –SO3H functionalized KIT-5 materials was successfully established. Moreover, the influence of both synthesis methods on the structural and textural parameters, as well as surface chemistry, morphology, and catalytic activity of –SO3H/KIT-5 materials was thoroughly investigated. The syntheses with 3-mepkaptopropyltrimethoxysilane (MPTMS) acting as a modifying agent resulted in samples in which functional groups were introduced into the structure and/or onto the mesoporous silica surface. The oxidation stage of –SH to –SO3H groups was carried out under mild conditions, using a “green” oxidant (H2O2). The application of different functionalization techniques and the introduction of different amounts of modifying agent allowed for an evaluation of the influence of these parameters on the ordering of the mesoporous structure of KIT-5 materials. The applied methods of assessment of the physicochemical parameters (XRD, low-temperature N2 sorption, TEM) showed that, especially when the co-condensation method was applied, as the number of functional groups increased, the ordering of structure characteristic of KIT-5 decreased. On the other hand, the samples modified by grafting had a stable structure, regardless of the amount of introduced MPTMS. Test reactions carried out on the basis of Friedel–Crafts alkylation process showed that the synthesized materials can be considered promising acid catalysts in heterogeneous catalysis reactions.