In the quest for a green economy, bioenergy has become a central component due to its ability to minimize depletion of natural energy resources and enhance environmental sustainability. However, the integration of bioenergy for a green economy has often led to policy resistance, the tendency for solutions to cause disastrous side effects on other aspects of the system that were not envisaged. The use of integrated model-based approaches for selection, design, and analysis of technological alternatives for bioenergy production would significantly enhance the systems'sustainability by optimizing design and operation, improving growth and profitability, and enabling a more synergistic interaction between the engineering and the macroeconomic aspects of bioenergy production systems. This chapter is designed to develop model-based methodological frameworks that will support sustainable decision making by all stakeholders involved in the design, operation, and commercialization of bioenergy production systems. Practical case studies are presented for bioethanol, biomethane, and synthetic gas production.