In the recent decade, the demand for alternative, sustainable, and energy-efficient alternatives has driven much attention in research and development on bioenergy production with nanocomposites owing to their distinctive physicochemical characteristics. The recent advancements in the synthesis of nanocomposites have markedly improved the efficiency for various bioenergy applications, such as biohydrogen, biomethane, bioethanol, and microbial fuel cells (MFCs). This chapter focuses highly on the systematically advanced synthesis procedures, including sol–gel processing, hydrothermal synthesis, electrospinning, green synthesis, and microwave-assisted techniques designed for the fabrication of highly functional nanocomposites. It also emphasizes directly toward the combination of metal/metal oxide nanoparticles with carbonaceous materials (e.g., graphene, carbon nanotubes, biochar), polymeric matrices, and biogenic substrates to enhance surface area, conductivity, and catalytic efficacy. An advancement in in situ hybridization, doping of noble metals, and morphological regulation has facilitated the effective development of nanocomposites with an improved electron transfer efficiency, greater biocompatibility, and extended operational stability in anaerobic and microbial environments. This chapter comprehensively explore the tunable physicochemical characteristics of synthesized nanocomposites with higher emphasis on the value of enhancement of enzyme immobilization, microbial adhesion, and electron shuttle efficiency with a critical consideration in improving the kinetics of bioenergy adaptation. Exclusive higher challenges in synthesis scalability, non-agglomeration, toxicity, and lifetime sustainability and recyclability were also addressed, with an opportunity for industrial applicability in alternate sustainable energy production. This Chapter is also strengthened by a retrospective review of recent experimental and computational investigations, highlighting structure-activity correlations and the mechanistic behavior of recent research insights from experiments. In the near future, an advancement in nanocomposite synthesis will signify a transformative change in material engineering for bioenergy systems, providing scalable and environmentally sustainable solutions aligned with the circular bio-economy.