Although different kinds of antibacterial formulas have been explored against bacterial infections, the development of both biocompatible and efficiently antibacterial matrices is still a challenge. In this study, we report a novel HPRP-A2 antimicrobial peptide/silk fibroin (SF) composite nanofibrous matrix fabricated by an all-aqueous electrospinning process (HPRP-A2 is an antibacterial peptide originated from Helicobacter pylori). The HPRP-A2/SF composite nanofibers had a round and smooth morphology. The incorporation of HPRP-A2 had little influence on both the morphology and biocompatibility of the SF nanofibers. Interestingly, the composite nanofibrous matrices showed an impressive antimicrobial activity against both Gram-positive and Gram-negative bacteria. Furthermore, the HPRP-A2/SF composite nanofibers showed excellent performance on accelerating healing of wound according to the data of animal experiment. Considering the facile and all-aqueous process, the HPRP-A2/SF composite nanofibrous matrices could be a promising candidate for antibacterial or wound management applications.