A comparative approach for the surface silylation of nanofibrillated cellulose (NFC) in water is proposed through an environmentally friendly sol-gel route based on alkoxysilanes. NFC suspensions were freeze-dried under controlled conditions in the presence of methyltrimethoxysilane used as a model alkoxysilane. Two different protocols that involve different pH values (0.4 and 4) and post-treatment procedures were investigated and compared. Protocol 1 led to a network of nanofibrils in which polysiloxane particles were dispersed, and protocol 2 produced a scaffold of cellulosic fibrils coated by a polysiloxane layer bonded firmly to the cellulosic substrate. Different from protocol 1, protocol 2 imparted the cellulosic material with hydrophobic properties and improved its thermal stability. Moreover, if 1 wt% of fibrils treated by protocol 2 were incorporated into a model polydimethylsiloxane network, substantial improvements of the static and dynamic mechanical properties of the composite were noted.