Blending with another biopolymer or nanomaterial can be an effective route to modify or tailor the properties of chitosan materials. In this work, we compared the effects of two nanoclays, montmorillonite (MMT) and sepiolite (SPT), on the properties of chitosan and chitosan/silk peptide (SP) films. While the solution-cast chitosan/SP films showed no phase separation on a micron length scale, some degree of molecular-level heterogeneity or incompatibility was evident. MMT nanoplatelets were delaminated in the chitosan-alone matrix, resulting in enhanced mechanical properties and hydrophobicity. In comparison, inclusion of SPT nanoneedles was less effective at altering the properties of the chitosan matrix. In the chitosan/SP system, the MMT was poorly dispersed, suggesting the two biopolymers interfere with how each interacts with the nanoclay. Nonetheless, in this case, MMT disrupted biopolymer chain interactions, leading to reduced mechanical properties and increased surface hydrophilicity. In contrast, SPT was found to enhance the mechanical properties of the chitosan/SP matrix, certainly associated with it being better dispersed. Thus, this work shows the efficacy of MMT and SPT as a route to altering the structure and properties of chitosan-based biopolymer matrices.