Polyhydroxybutyrate (PHB) is a natural polyester synthesized by several microorganisms. Moreover, it has excellent biodegradability and is an eco-friendly material because it converts water and carbon dioxide as final decomposition products. However, the applications of PHB are limited because of its stiffness and brittleness. Because cellulose nanocrystals (CNCs) have excellent intrinsic mechanical properties such as high specific strength and modulus, they may compensate for the insufficient physical properties of PHB by producing their nanocomposites. In this study, natural polyesters were extracted from Cupriavidus necator fermentation with CNCs, which were well-dispersed in nitrogen-limited liquid culture media. Fourier-transform infrared spectroscopy results revealed that the additional O–H peak originating from cellulose at 3500–3200 cm−1 was observed for PHB along with the C=O and –COO bands at 1720 cm−1. This suggests that PHB–CNC nanocomposites could be readily obtained using C. necator fermented in well-dispersed CNC-supplemented culture media.