Polyhydroxybutyrate (PHB) is a carbon reserve in some bacteria and under nutrient-limiting conditions, accumulates intracellularly in the form of inclusion bodies. These inclusions contain proteins, and the PHB within the inclusions exists in an amorphous state. In this study, a procedure to recover native PHB inclusions was developed, and the isolated inclusions characterized using ¹³C NMR, western blotting, atomic force microscopy and fluorescence microscopy. High resolution images of native PHB granules were obtained and the surface features and dimensions of the granules analysed. The size, morphology and composition of the PHB inclusions are important parameters for analysing inclusions formed within PHB-producing oil palm to support commercial objectives. The methods reported in this work support the development of analytical techniques for transgenic bioplastic-producing oil palm samples.