Microcrystalline cellulose (MCC) has unique properties and its use as reinforcement for polymer composites has been increasing. However, the intrinsic incompatibility with most polymers requires surface modification to improve chemical compatibility prior to its incorporation into a polymer. In this paper, an in-depth study of silanization of MCC using 3-aminopropyltriethoxysilane (APTES), at different concentration, was done. The grafting amount of APTES onto MCC was determined by different methods: from residual mass and from nitrogen content. Solid-state 13C and 29Si nuclear magnetic resonance (NMR), field emission scanning electron microscopy with energy dispersive X-ray (SEM-EDX), spectroscopy plasma optical emission spectrometry (ICP), and a deep study of structural properties by X-ray diffraction were carried out. A better correlation for grafting amount of APTES onto MCC was observed for nitrogen content method than residual mass according the Pearson’s correlation. 13C NMR revealed all the carbon structures from cellulose and from APTES molecules and 29Si NMR revealed D, T and Q Si structures. The silane treatment did not alter the shape of MCC and all treated samples showed Si characteristic peak at ~ 1.75 kEv. From ICP was observed higher Si content before MCC addition than after, evidencing, once again, APTES grafting. The exposure to APTES in acidic medium caused several effects on the MCC, splitting larger Iβ crystallites in half and along the more reactive hydrophilic sides. The diameter of the smaller IVI crystallites was largely reduced by the treatment, especially when the silane concentration was 1:5 (m/v), above which the diameter increases again.