Copper nanoparticles (CuNPs) and palladium nanoparticles (PdNPs) have attracted wide attention owing to their multifaceted utility in catalysis, sensors, and biomedical applications. Their therapeutic spectrum includes anticancer, antiviral, antibacterial, antifungal, antidiabetic, antioxidant potential which rationalizes the exploration of diverse physical, chemical, and biological routes for fabrication. In this article, we focused on bacterium-assisted design of nanostructured copper and palladium for applications in therapy against multidrug-resistant pathogens, dehalogenation of diatrizoate, Heck coupling of iodobenzene, polymer electric membrane fuel cell, metal recovery, and electronic waste management. Further, hypothesis behind microbial synthesis of PdNPs in E. coli containing [NiFe] hydrogenase Hyd-1 is discussed. Similarly, detailed mechanism of synthesis and stabilization in Cyanobacteria is also documented. Both CuNPs and PdNPs act as potent chemotherapeutic agents that can further be enhanced by conjugation with drugs and/or fluorophores and ligands for simultaneous diagnosis and targeted drug delivery to the cancer site or infection. These bacteriogenic nanoparticles can be used in sensors and pollution control.