The accelerating global demand for sustainable energy, driven by population growth, industrialization, and environmental concerns, has intensified the search for renewable alternatives to fossil fuels. Biofuels, including bioethanol, biodiesel, biogas, and biohydrogen, offer a viable and practical pathway to reducing net carbon dioxide (CO₂) emissions. Yet, their large-scale production remains constrained by biomass recalcitrance, high pretreatment costs, and the enzyme-intensive nature of conversion processes. Recent advances in enzyme immobilization using magnetic nanoparticles (MNPs), covalent organic frameworks, metal–organic frameworks, and biochar have significantly improved enzyme stability, recyclability, and catalytic efficiency. Complementary strategies such as cross-linked enzyme aggregates, carrier-free immobilization, and site-specific attachment further reduce enzyme leaching and operational costs, particularly in lipase-mediated biodiesel synthesis. In addition to biocatalysis, nanozymes—nanomaterials exhibiting enzyme-like activity—are emerging as robust co-catalysts for biomass degradation and upgrading, although challenges in selectivity and environmental safety persist. Green synthesis approaches employing plant extracts, microbes, and agro-industrial wastes are increasingly adopted to produce eco-friendly nanomaterials and bio-derived supports aligned with circular economy principles. These functionalized materials have demonstrated promising performance in esterification, transesterification, and catalytic routes for biohydrogen generation. Technoeconomic and lifecycle assessments emphasize the need to balance catalyst complexity with environmental and economic sustainability. Multifunctional catalysts, process intensification strategies, and engineered thermostable enzymes are improving productivity. Looking forward, pilot-scale validation of green-synthesized nano- and biomaterials, coupled with appropriate regulatory frameworks, will be critical for real-world deployment.