The biocomposite systems based on mesoporous MCF silica support and protein molecules are characterized with regard to their surface, topographic, thermal properties. Mesoporous silica materials (MCF) covered by the adsorbed protein molecules (BSA and OVA) were examined and characterized by using various techniques including X-ray diffraction, the Fourier transform infrared spectroscopy with attenuated total reflectance, X-ray photoelectron spectroscopy and scanning electron microscopy with microanalysis. The results of study focused on a detailed analysis of microstructure (topography, texture), and chemistry (chemical bonds, functional groups, elemental composition) of protein/mesoporous silica biocomposite. Moreover, the thermal properties of prepared biomaterials were investigated by means of TG/DSC-FTIR-MS-coupled technique. These powerful methods provided detailed information for understanding protein adsorption on MCF. Significant differentiation in surface chemistry and topography of MCF material was observed after protein adsorption. Basing on the results of thermal analysis stronger changes of the surface properties and more stable interactions of biomolecules with MCF-d16 support were observed for larger BSA molecules compared to smaller ovalbumin ones.