The aim of this study was to investigate the effects of cellulose nanofibrils and nanoclays on the mechanical, thermal, and morphological properties of polyhydroxybutyrate and polylactic acid bio-polymers. Polyhydroxybutyrate and polylactic acid as a polymer matrix and nanoclays and cellulose nanofibrils as reinforcing nano-fillers were used to prepare the biopolymer nanocomposites in twin screw extruder. Density, flexure strength and flexure modulus, tensile strength and tensile modulus, impact strength, thermal properties, and morphological characterization of the obtained biopolymer nanocomposites were determined. According to the obtained results, densities of the biopolymer nanocomposites were found to decrease with addition of the bio-fillers, and it was determined to be decreasing the density due to increasing the porosity in biopolymer nanocomposites. Although the increasing in the porosity of biopolymer nanocomposites was found in scanning electron microscope pictures, the mechanical properties of the biopolymer nanocomposites generally increased as compare with neat bio-polymers. Thermal analysis conducted with thermogravimetric-dynamic thermal analysis and differential scanning calorimeter showed that thermal stability of the biopolymer nanocomposites generally improved according to the neat bio-polymers.