Bacterial infections pose a serious worldwide public health concern and play an important role in slowing or dramatically delaying wound healing. However, traditional antibiotics are faced with obstacles such as bacterial resistance and unsatisfactory biocompatibility, which has impeded further clinical translation. In recent years, antimicrobial nanomaterials have emerged as viable alternatives for combating bacterial infections, and carbon dots (CDs) have received particularly widespread attention due to their superior characteristics. In this work, a simple and eco-friendly one-step hydrothermal method was employed using the natural herbal medicine Eucommia ulmoides as a biomass carbon source to synthesize an Fe-doped CDs nanozyme (Fe-CDs) with good peroxidase-like (POD-like) activity, high biocompatibility, and strong antimicrobial activity for safe and effective antimicrobial therapy and the promotion of wound healing. L929 cells co-cultured with Fe-CDs did not show significant cytotoxicity and favored cell proliferation at appropriate concentrations. In addition, Fe-CDs catalyzed the decomposition of low-concentration H2O2 to ·OH, leading to enhanced antimicrobial activity. Both in vitro and in vivo experiments demonstrated that Fe-CDs exhibit potent antibacterial properties, the ability to promote cell migration and angiogenesis, and significant potential for promoting the healing of infected wounds. In summary, a green and safe antimicrobial nanozyme based on a biomass herbal medicine was developed in this work, offering promising insight into the development of novel antimicrobial materials and tissue regeneration engineering.