The results of this study will help in guiding the future design of low-cost and highly performing functionalized mesoporous silica using cationic surfactants as directing agents. Indeed, by properly tuning surface interactions and the textural characteristics, the overall efficiency of H2 capture processes could be improved. Among different synthetized samples, the experimental results show the better interaction with (3-Aminopropyl)triethoxysilane precursor. Furthermore, an NMR investigation aiming at clarifying the internal arrangement and diffusion properties of hydrogen molecules inside functionalized porous silica materials has been performed. The NMR spectral analysis and the T1 relaxation times indicated two different “populations” for H2 sorbate due to the molecules adsorbed in mesopores and in micropores. For the first time, the H2 self-diffusion coefficient in functionalized silica has been experimentally measured by pulsed field gradient NMR. The spin-echo decay revealed two different diffusion mechanisms coexist in the functionalized mesoporous silica, except for the material functionalized with iodopropyl groups, which shows a single diffusion coefficient.