Organic-inorganic mesoporous materials of the MCM-41 type are important materials that can be prepared by either post-synthesis or one-pot synthesis procedures. A complete control of the characteristics at a local level is of the utmost importance in view of the applications of such materials. However, there are not many studies relating such features with synthetic approaches. In this work, we prepared samples by post-synthesis derivatization of materials from Si-based MCM-41, with bidentate nitrogen ligands bearing one or two silylated arms, and by one-pot synthesis of organic-inorganic hybrid materials. The bulk properties of the two kinds of materials were comparable. Diffuse reflectance infrared Fourier transform (DRIFT) spectroscopy and Raman spectroscopy were used to investigate the local environment, namely, the number of OH groups and distribution of SiO(4) units (large and small ring units). Hydrophilicity correlates with both the type of organic moiety used (mono- or disilylated), as well as with the synthetic procedure. The same vibrational studies showed how the structure in the channels changes as a function of pressure, reflecting the low mechanical stability of the mesoporous materials.