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The current study attempts to evaluate the formation, morphology, and physico-chemical properties of zinc oxide nanoparticles (ZnO NPs) synthesized from Clinopodium vulgare extract at different pH values and to investigate their antimicrobial and biomedical application potential. The reduction of zinc ions to ZnO NPs was determined by UV spectra, which revealed absorption peaks at 390 nm at pH 5 and 348 nm at pH 9, respectively. The spherical morphology of the nanoparticles was observed using scanning electron microscopy (SEM), and the size was 47 nm for pH 5 and 45 nm for pH 9. Fourier-transformed infrared spectroscopy (FTIR) was used to reveal the presence of functional groups on the surface of nanoparticles. The antibacterial activity was examined against Staphylococcus aureus, Streptococcus pyogenes, and Klebsiella pneumonia via the agar-well diffusion method. Comparatively, the highest activities were recorded at pH 9 against all bacterial strains, and among these, biogenic ZnO NPs displayed the maximum inhibition zone (i.e., 20.88 ± 0.79 mm) against S. aureus. ZnO NPs prepared at pH 9 exhibited the highest antifungal activity of 80% at 25 mg/mL and antileishmanial activity of 82% at 400 mg/mL. Altogether, ZnO NPs synthesized at pH 9 show promising antimicrobial potential and could be used for biomedical applications.