In recent decades, nanotechnology is growing rapidly owing to its widespread application in medical science. The aim of the experiment was the evaluation of cytotoxicity, antioxidant, antibacterial, antifungal, and cutaneous wound healing activities of green synthesized manganese nanoparticles using Ziziphora clinopodioides Lam leaves (MnNPs@ZC). The synthesized MnNPs@ZC were characterized using different techniques including UV–Vis., FT‐IR spectroscopy, X‐ray diffraction (XRD), scanning electron microscopy (SEM), and energy dispersive X‐ray spectrometry (EDS). According to the XRD analysis, 48.10 nm was measured for the crystal size of nanoparticles. SEM images exhibited a uniform spherical morphology and size in the range of 47.58 to 70.26 nm for the biosynthesized nanoparticles. MnNPs@ZC revealed excellent non‐cytotoxicity effect against human umbilical vein endothelial cells, antioxidant activity against DPPH, antibacterial properties against Gram‐negative bacteria (Salmonella typhimurium, Pseudomonas aeruginosa, and Escherichia coli O157:H7) and Gram‐positive bacteria (Streptococcus pneumonia, Staphylococcus aureus, and Bacillus subtilis), and antifungal potentials against Candida glabrata, Candida albicans, Candida guilliermondii, and Candida krusei. Also, use of MnNPs@ZC ointment decreased significantly (p ≤ 0.01) the wound area, total cells, neutrophil, and lymphocyte and raised significantly (p ≤ 0.01) the wound contracture, hydroxyl proline, hexosamine, hexuronic acid, fibrocyte, and fibrocytes/fibroblast rate compared to other groups in experimental animals. In conclusion, synthesized MnNPs@ZC indicated antibacterial, antifungal, non‐cytotoxicity, antioxidant, and cutaneous wound healing effects in a dose‐depended manner. After confirming in the clinical trials, these nanoparticles can be used in human for the treatment of cutaneous and infectious diseases.