Despite promising characteristics such as the biodegradability and the environmentally-benign nature of cellulose nanocrystal (CNC) based composites, their poor dispersion and agglomeration in thermoplastic matrix during the melting process is a “bottleneck” in the development of these composites. In this work, a cylindrical atmospheric pressure dielectric barrier discharge (AP-DBD) was employed to functionalize CNCs to reduce their surface hydrophilicity and improve their dispersion in polar organic solvents. Three different gas mixtures were used for plasma treatment, argon/methane, argon/silane and an argon/methane followed by argon/silane. In all cases, the plasma treatment was conducted below 90°C as determined from optical emission spectroscopy (OES) analysis. The x-ray diffraction (XRD) analysis of both raw and plasma treated CNC powders confirms that the CNC crystallographic properties remain unchanged after plasma treatment. Fourier transform infrared (FTIR) spectroscopy and X-ray photoelectron spectroscopy (XPS) analysis reveal the presence of hydrophobic C-Hx moieties on the CNC granular surface after argon/methane plasma treatment whereas SiHx, Si-O-Si, SiC bonds were formed after argon/silane plasma treatment. Under these experimental conditions, water wettability tests reveal some significant water repellency of the naturally hydrophilic cellulosic raw material. Moreover, the formation the SiHx moieties in silane-treated CNCs clearly enhances the hydrophobicity of the CNC powder in contrast to the sole C-Hx moieties synthetized by argon/methane plasma. High-resolution SEM images indicate the presence of agglomerated granules with 5-10 µm diameters in size. The surface functionalities of CNC powder enhance its dispersibility in polar solvents. Overall, this study emphasizes that AP-DBDs are suitable to process thermo-sensitive CNCs.