Cellulose nanocrystals (CNCs) synthesized from microcrystalline cellulose by acid hydrolysis were added into poly(lactic acid)–poly(hydroxybutyrate) (PLA–PHB) blends to improve the final properties of the multifunctional systems. CNC were also modified with a surfactant (CNCs) to increase the interfacial adhesion in the systems maintaining the thermal stability. Firstly, masterbatch pellets were obtained for each formulation to improve the dispersion of the cellulose structures in the PLA–PHB and then nanocomposite films were processed. The thermal stability as well as the morphological and structural properties of nanocomposites was investigated. While PHB increased the PLA crystallinity due to its nucleation effect, well dispersed CNC and CNCs not only increased the crystallinity but also improved the processability, the thermal stability and the interaction between both polymers especially in the case of the modified CNCs based PLA–PHB formulation. Likewise, CNCs were better dispersed in PLA-CNCs and PLA–PHB–CNCs, than CNC.