Abstract Non-flocculating aqueous suspensions of cellulose nanocrystals with different sizes were prepared by the combination of acid hydrolysis and surface TEMPO oxidative carboxylation of cotton linter and microfibrils of parenchyma cell cellulose (PCC). A decrease of the crystal size occurred and the introduction of negative charges at the interface of the crystalline domains induced a better individualization of the crystallites. These suspensions were further amidated by interaction with 4-amino TEMPO; a nitroxide radical containing a terminal amino group. The products were characterized by elemental analysis, conductimetry, solid-state 13C NMR, FTIR and EPR spectroscopies, together with X-ray diffraction analysis and the coupling performance was deduced with a high correlation. The results indicated that the amidation was effective with yield roughly of 30%, the reaction yield being somewhat more important on samples from cotton origin. In all samples, the amidation was realized at the surface of the samples from carboxylated functions, which kept their intrinsic crystallinity, integrity and perfection throughout the preparation protocol. Their hydrophobic character was evaluated by observing their behavior in polar and non-polar solvents.