The world’s quest for sustainable and carbon-neutral sources of energy has placed microbial biotechnology for bioenergy as one of the most important and promising technologies of the twenty-first century. In this chapter, the use of microbes as efficient biocatalysts for the transformation of renewable biomass sources, including agricultural waste and non-food crops, into a wide range of alternative energy carriers is discussed. Going beyond biofuels that are traditionally based on corn ethanol, some advanced microbial conversion processes, such as anaerobic digestion for biogas production, dark fermentation for biohydrogen production, and microbial electrochemical technologies for power generation. We will also discuss the role of microorganisms in the production of higher-order liquid biofuels (biodiesel, biobutanol) and energy-rich molecules such as biohydrogen and polyhydroxyalkanoates (PHAs) using lignocellulosic, agro-industrial effluents, and algal biomass. Much emphasis is given to the “waste-to-wealth” trend: agricultural residues (straw, stover, manure, and processing waste) can indeed be transformed into energy, contributing to waste management, improving energy security, and farm-level economics. The chapter also discusses the key issues involved, including feedstock pre-treatment, process scalability, and cost feasibility, and finally, provides future perspectives on synthetic biology and metabolic engineering approaches for the development of robust microbial cell factories for improved bioenergy production. This synthesis aims to offer researchers, students, and policymakers alike an all-in-one resource demonstrating that microbes are the drivers of a circular bioeconomy and a sustainable energy future.