Nanoparticles based on cellulose nanocrystals (CNC) and montmorillonite clay (MMT) were prepared using spray freeze-drying. The nanoparticles were then used as reinforcement to prepare nanocomposites with poly(lactic acid) (PLA) as the polymer matrix. The effect of spray freeze-dried CNC (SFD-CNC) and spray freeze-dried MMT (SFD-MMT) on the rheological and mechanical properties of PLA and its blends with poly[(butylene succinate)-co-adipate)] (PBSA) were investigated. An epoxy chain extender was used during preparation of the blends and nanocomposites to enhance the mechanical properties of the products. Different methods such as scanning electron microscopy, X-ray diffraction and adsorption/desorption analyses were used to characterize the prepared nanoparticles and their localization in the blends. Dynamic oscillatory shear behavior, elongational viscosity and mechanical characteristics of the nanocomposites of PLA and the blends were evaluated. The results obtained for nanocomposites filled with unmodified SFD-MMT were compared with those obtained when the filler was a commercial organically modified montmorillonite nanoclay (methyl-tallow-bis(2-hydroxyeethyl) quaternary ammonium chloride) (C30B), which was not spray freeze-dried.