It is a common pursuit to create an efficient photodynamic therapy (PDT), as a potential alternative to antibiotics. In this research, we first discovered and acquired the natural outer membrane vesicles (OMVs) from Serratia marcescens for effective photodynamic inactivation of both bacteria and fungi. The native OMVs was prepared from the culture media of S. marcescens, which inherently contained a photosensitizer named prodigiosin (PG). The negatively-charged, green-emitting OMVs exhibited improved water-solubility and increased singlet oxygen generation, as compared to free PG, resulting in notably enhanced antibacterial PDT effect towards microbes with appealing biosafety in vitro. Upon binding to the microbial cells through hydrophobic interaction, OMVs enriched PG in the microbic cells, destroying cell membrane structure and DNA and causing protein leakage under light irradiation, leading to microbial cell death. More importantly, OMVs could notably enhance infected wound healing and antibacterial effectiveness with satisfactory biocompatibility in mice. Collectively, the naturally-occurring PG-containing OMVs offers a novel modality for effective antimicrobial PDT, benefiting the treatment of microbial infection in clinic.