Cellulose nanocrystals (CNCs) and/or sepiolite (SPT) were thermomechanically mixed with un-plasticised chitosan and chitosan/carboxymethyl cellulose (CMC) blends plasticised with 1-ethyl-3-methylimidazolium acetate ([C2mim][OAc]). Examination of the morphology of these materials indicates that SPT aggregates were reduced when CNCs or [C2mim][OAc] were present. Inclusion of CNCs and/or SPT had a greater effect on material properties when the matrices were un-plasticised. Addition of SPT or CNCs altered the crystalline structure of the un-plasticised chitosan matrix. Moreover, a combination of SPT and CNCs was more effective at suppressing re-crystallisation. Nonetheless, the mechanical properties and surface hydrophobicity were more related to CNC/SPT–biopolymer interactions. The un-plasticised bionanocomposites generally showed increased relaxation temperatures, enhanced tensile strength, and reduced surface wettability. For the [C2mim][OAc] plasticised matrices, the ionic liquid (IL) dominates the interactions with the biopolymers such that the effect of the nanofillers is diminished. However, for the [C2mim][OAc] plasticised chitosan/CMC matrix, CNCs and SPT acted synergistically suppressing re-crystallisation but resulting in increased tensile strength.