This study investigates the morphology control and antibacterial properties of copper and silver nanoparticles. Nanoparticles were synthesized using sodium borohydride, agar, and plant extract methods. The particle size and dispersion were analyzed by transmission electron microscopy (TEM), while the reactive components in plant extracts were examined by high-performance liquid chromatography (HPLC). Copper nanoparticles prepared via the plant extract method exhibited higher stability, smaller particle size, and a distinct Tyndall effect. In contrast, silver nanoparticles tended to aggregate due to high reactant concentrations and insufficient stabilizers. The copper nanoparticles showed significant inhibitory effects against Escherichia coli, whereas the antibacterial activity of silver nanoparticles was more sensitive to particle size. After Corona discharge treatment, the number of silver nanoparticles increased, their particle size decreased, and their antibacterial activity improved. Comparison among Corona discharge, plasma, and low-power laser post-treatment processes revealed that all effectively reduced particle size; however, excessive energy caused thermal expansion, resulting in particle growth. Through a surface-contact decomposition mechanism, the plasma process efficiently refines silver nanoparticles, achieving smaller and more uniform particle sizes that lead to enhanced antibacterial activity. After 5 minutes of treatment, the antibacterial performance exceeded that of penicillin. This work integrates green synthesis with energy-assisted post-processing, offering new insights into the fabrication and antibacterial use of copper and silver nanoparticles.