The growing challenge of antibiotic resistance has prompted the search for cost-effective and efficient alternatives. Developing new synthetic or natural antimicrobial drugs is often resource-intensive and time-consuming, leading current research to focus on plant-based extracts and nanoparticle synthesis capable of generating reactive oxygen species or forming metal complexes. This study aims to optimize the eco-friendly synthesis of silver (AgNPs) and zinc oxide nanoparticles (ZnO NPs) with antibacterial properties for topical application. A standardized ethanolic extract of Paeonia anomala was used as a reducing and stabilizing agent. Phytocomplex formation with zinc ions under various pH conditions was modeled using Medusa software. The effects of microwave, UV irradiation, and ultrasound on nanoparticle synthesis and stability were assessed. Physicochemical characteristics and colloidal stability were monitored via UV-Vis spectrophotometry, with surface plasmon resonance (SPR) peaks observed at 408 nm for AgNPs and 320 nm for ZnO NPs, confirming nanoscale formation. Particle size and zeta potential were also evaluated. Storage at room temperature led to slightly more aggregation compared to refrigeration at 4 °C, though the effect was minimal. Neither the Paeonia anomala tincture nor the AgNPs derived from it exhibited antioxidant activity. However, AgNPs synthesized with the extract and stabilized via ultrasound demonstrated strong antimicrobial activity against Staphylococcus aureus and Escherichia coli at concentrations as low as 0.015 mM, while ZnO NPs required at least 2 mM to achieve similar effects.