Kaolinite is often used as a base for the synthesis of new organo-mineral nanomaterials designed for applications in industry and in environmental protection. To make the mineral structure more likely to interact with organic molecules, a kaolinite-methanol complex (KM) can be used. In the present study, different experimental procedures were tested to investigate the formation of the KM. The kaolinite-dimethyl sulfoxide intercalation compound (KDS), either wet or dried, was used as a pre-intercalate. The samples obtained were characterized using X-ray diffraction, Fourier-transform infrared spectroscopy, CHNS elemental analysis, 13C CP-magic angle spinning nuclear magnetic resonance (MAS NMR), and 27Al and 29Si MAS NMR techniques. The method of density functional theory with dispersion corrections (DFT-D2) was used to explain the structure and to simulate the vibrational spectra of KM. Theoretical results were compared with experimental data. The most effective formation of the KM (d001 = 11.1 Å – wet; d001 = 8.7 Å – dried) was observed when the dried KDS precursor was used. In such conditions the degree of intercalation reached ~98% after 24 h of reaction time. As indicated by the CHNS elemental analysis, ~⅙ of the inner-surface OH groups were grafted by OCH3 groups. The esterification reaction was less efficient at higher temperatures or when wet KDS was used. In the latter case, the excess of very polar dimethyl sulfoxide molecules prevented intercalation of methanol and further grafting. Detailed analysis of the results of theoretical simulations revealed that the reaction of the KDS with methanol led to the formation of kaolinite with both grafted methoxy groups and intercalated methanol, and water molecules in the interlayer space. The spectra calculated revealed the contribution of individual vibrational modes into the complex bands, i.e. the energy of C–H vibrations was in the order: νasCHmet > νasCHmtx > νsCHmet > νsCHmtx.