Display omitted •Functionalized cellulose nanocrystals (CNCs) for dye absorption.•Selective binding of methylene blue by polydopamine-CNC.•ITC analysis confirmed the types of binding interactions. In this study, cellulose nanocrystals (CNCs) were evaluated as potential adsorbents for the selective adsorption and separation of organic dyes mixtures (methylene blue (MB), with either methyl orange (MO) or rhodamine b (RB) or crystal violet (CV)). The role of surface functional groups on the dye-CNC interaction was examined using pristine and surface-functionalized CNCs, such polydopamine (PD) and melamine–formaldehyde (MF) coated CNCs (PD-CNCs and MF-CNCs respectively). Batch adsorption studies on MB/MO dye mixture showed that pristine CNCs bearing anionic sulfate ester groups exhibited preferential adsorption for MB, with a 85.78% adsorption efficiency. This preferential adsorption was further enhanced in the case of PD-CNCs, which showed 100% adsorption efficiency for MB. Additional studies on MB/RB and MB/CV dye mixtures confirmed that the improved selectivity of PD-CNCs towards MB is associated with the synergistic binding interactions, such as electrostatic attraction, π-π stacking, and hydrogen bonding. MF-CNCs with cationic amine groups displayed selective binding towards MO, an anionic dye. Also, PD-CNCs and MF-CNCs were found to completely separate MB and MO from a diluted MB/MO dye mixture. Isothermal titration calorimetry and dye flocculation experiments confirmed that the selective binding is associated with the surface-functionality of CNCs.