Bacterial cellulose (BC) with increased hydrophobicity is required for several applications including packaging. Surface functionalization of BC may provide good resistance to moisture, increased barrier properties or improved compatibility to polymer matrices. For this purpose, chemical grafting of BC in mild, eco-friendly conditions was carried out using different agents. BC membranes were surface functionalized with vinyl-triethoxy silane (VS) or 3-aminopropyl triethoxysilane (APS), by acylation and acrylation. The efficiency of the surface treatments was highlighted by Fourier transform infrared spectroscopy and X-ray photoelectron spectroscopy, by contact angle measurements and by dynamic mechanical analysis. The morphological investigation by atomic force microscopy and scanning electron microscopy revealed an increased compactness for surface functionalized BC, which correlated well with the different increase of the contact angle. BC treated with APS and VS showed more than a twofold increase in contact angle value. Similarly, the crystallinity degree was reduced to 69.6% and 72.9% after APS and VS treatments as compared with 84.1% for untreated BC, confirming the grafting reaction and the decrease in hydrogen bonding. All the applied treatments delayed the degradation of BC. However, the highest increase in thermal stability was observed for silanes treated membranes. Effective, eco-friendly methods for improving the surface hydrophobicity of bacterial cellulose for food packaging were proposed in this study.