The conductivity and high surface-to-volume ratio of carbon nanofibers (CNFs) composited with the medium-chain-length poly-3-hydroxyalkanoate (mcl-PHA) have attracted much attention as smart biomaterial. However, poor CNF dispersion leads to tactoid agglomerated composite with poor crystallite morphology resulting in inferior thermomechanical properties. We employed acoustic sonication to enhance the construction of exfoliated PHA/CNFs nanocomposites. The effects of CNF loading and the insonation variables (power intensity, frequency, and time) on the stability and microscopic morphology of the nanocomposites were studied. Sonication improved the dispersion of CNFs into the polymer matrix, thereby improving the physical morphology, crystallinity, and thermomechanical properties of the nanocomposites. For example, compositing the polymer with 10% w/w CNF resulted in 66% increase in crystallite size, 46% increase in micromolecular elastic strain, and 17% increase in lattice strain. Nevertheless, polymer degradation was observed following the ultrasound exposure. The constructed bionanocomposite could potentially be applied for organic electroconductive materials, biosensors and stimuli-responsive drug delivery devices.