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Engineering the molecular assembly at biomolecular interface is one of the prevailing techniques in synthetic biology to derive novel supramolecular structures. In this study, we have biofunctionalized polyoxometalates with peptide-based cationic polymer. Surface functionalization of polyoxometalates (POMs) results in derivation of self-assembled polymer–POM nanocomposites with novel antifungal activity. Electron rich POM triggers the morphological alteration in molecularly enriched β-sheet peptide polymer promoting the evolution of nanorods. Due to the inherited biocidal properties of the cationic polymer and the POM, the nanorods exhibit enhanced antifungal activity highlighting the significance of combinatorial systems in advanced drug therapeutics.