Description: Highlights: • Using a vHPO is efficient in increasing chemical diversity of natural extracts. • vHPO are a sustainable strategy to catalyze unspecific halogenation. • Metabolomics and bioinformatics are effective tools to highlight relevant molecules. • 12-bromo-communesin A is a novel brominated molecule with antimicrobial activity. This study reports for the first time the use of a vanadium chloroperoxidase (vCPO) enzyme to increase the chemical diversity of marine fungal extracts to generate new natural chemical entities. The vCPO used is a recombinant protein from the marine fungus Hortaea werneckii (HwvCPO). It catalyzes the formation of hypohalous acid (HOX), a highly reactive compound that can react with electron-rich substrates. Here, four fungal extracts obtained from different marine fungal strains (Penicillium expansum, Aspergillus pseudoglaucus, Trichoderma sp. and Hortaea werneckii) were investigated for enhancement of their chemical diversity. The metabolomic study showed that the enzymatic treatment of extracts of P. expansum and A. pseudoglaucus significantly boosted the chemodiversity by increasing the number of halogenated molecules. Indeed, respectively 5.07 and 6.65 times more halogenated ions were detected in ESI-MS profile of the extracts compared to negative controls. The new chemistry generated allowed the identification of new brominated compounds, one of which was further purified and characterized as 12-bromo-communesin A (2). This new compound, in contrast to communesin A (1), exhibited moderate antimicrobial activity on the methillicin-resistant Staphylococcus aureus (IC50 of 62 μM). This study has clearly demonstrated the employment of the vCPO enzyme to be a promising and environmentally friendly strategy to enhance the chemical diversity of natural extracts.