The purpose of this experiment was the green synthesis of silver nanoparticles from aqueous extracts of Ziziphora clinopodioides Lam (AgNPs@Ziziphora) and assessment of their cytotoxicity, antioxidant, antibacterial, antifungal, and cutaneous wound‐healing effects. These nanoparticles were characterized using ultraviolet–visible spectroscopy (UV–Vis), X‐ray diffraction (XRD), field emission scanning electron microscopy with energy‐dispersive X‐ray spectroscopy (FESEM‐EDX), atomic force microscopy (AFM), and transmission electron microscopy (TEM). UV–Vis, TEM, and FESEM analyses indicated that the size of Ag nanoparticles (AgNPs) depended on Z. clinopodioides and AgNO3 concentrations. In vitro biological experiments indicated that AgNPs@Ziziphora has excellent antioxidant potential against DPPH, antifungal effects against Candida guilliermondii, Candida krusei, Candida glabrata, and Candida albicans, and antibacterial activities against Staphylococcus aureus, Bacillus subtilis, Streptococcus pneumonia, Salmonella typhimurium, Pseudomonas aeruginosa, and Escherichia coli O157:H7. Also, these nanoparticles did not exhibit cytotoxicity property against human umbilical vein endothelial cells (HUVECs). An in vivo biological test revealed that AgNPs@Ziziphora ointment significantly (p ≤ 0.01) increased the levels of wound contracture, blood vessels, hydroxyl proline, hexuronic acid, hexosamine, fibrocytes, fibroblasts, and fibrocyte/fibroblast ratio and significantly (p ≤ 0.01) decreased the wound area, and levels of total cells, neutrophils, and lymphocytes than other groups in rats. The results of UV–Vis, XRD, FESEM‐EDX, AFM, and TEM confirmed that the aqueous extract of Z. clinopodioides can be used to produce silver nanoparticles with significant antioxidant, antimicrobial, and cutaneous wound‐healing properties without any cytotoxicity.