The recent emergence of bio-based nanocomposites makes perfect sense from a technical and environmental point of view. Cellulose nanocrystals (CNCs) are novel bio-based nanomaterials with a wide range of beneficial properties. Their biodegradability, crystallinity, high surface area, and mechanical strength, as well as their highly reactive surface, make them ideal materials as nanofillers in polymeric matrices. However, most the bio-based polymers are hydrophobic, and the hydrophilicity of CNC is therefore a challenge to their incorporation in such matrices. In this study, a new procedure for surface modification of CNC with long aliphatic chains [lauric acid (12 carbons) and stearic acid (18 carbons)] was developed that limits the use of petro-chemicals and facilitates their potential recycling. A study of the dispersion state of CNC in acetone was performed first. Then, grafting efficiency was highlighted by several techniques and quantification of the amount of grafted fatty chains was investigated. Degrees of substitution on the bulk and on the surface of the CNC were calculated between 0.1 and 0.3, which provided enough grafted functions to confer hydrophobic behavior to modified CNCs, as highlighted by the increasing of contact angle from 65° for neat CNC to 80° after modification. Finally, conservation of CNC crystalline structure and morphology was proved by both X-ray diffraction and transmission electron microscopy analyses. Modified CNCs exhibit a crystallinity index close to 86% and length of approximately 350 nm. Thus, crystalline hydrophobic cellulosic nanomaterials were prepared using a more environmentally friendly procedure than those classically found in the literature.