The concept of “Industrial Biosystems Engineering (IBE)” was proposed by the author as a framework of scientific knowledge and methodology of a new branch of engineering serving the needs for the upcoming bioeconomy that requires a biorefinery and biomanufaturing of commodity fuel and chemicals at industrial production scale. The key disciplinary support for this new engineering branch includes basic systems biology, bioprocess engineering, and systems engineering and systems analysis. This presentation discusses the relationship between the IBsE and existing disciplines and provides examples of the IBE application to biofuel and biochemical production. Developing such a framework offers a great opportunity for applying systems engineering theory and approach to biorefinery analysis and design for supporting the development of the bioeconomy.