Cellulose nanocrystals (CNCs) are valuable nanomaterials obtained from renewable resources. Their properties make them suitable for a wide range of applications, including polymer reinforcement. However, due to their highly hydrophilic character, it is necessary to modify their surface with non-polar functional groups before their incorporation into a hydrophobic polymer matrix. In this work, cellulose nanocrystals were modified using a silane coupling agent and choline lactate, an ionic liquid derived from renewable resources, as a reaction medium. Modified cellulose nanocrystals were characterized by infrared spectroscopy, showing new peaks associated to the modification performed. X-ray diffraction was used to analyze the crystalline structure of functionalized cellulose nanocrystals and to optimize the amount of silane for functionalization. Poly(lactic acid) (PLA) nanocomposites containing 1 wt % of functionalized cellulose nanocrystals were prepared. They were characterized by field-emission scanning electron microscopy (FE-SEM) and mechanical tests. The use of choline lactate as reaction media has been shown to be an alternative method for the dispersion and silanization of the cellulose nanocrystals without the addition of an external catalyst.