A simple chemical reduction method was employed to synthesize Cu-Ag and Ag-Cu core-shell nanostructures inside polyvinyl alcohol (PVA) matrix at room temperature. The core-shell nanostructures have been synthesized by varying the two different concentrations (i.e. 0.1 and 0.01 M) of the respective metal ions in equimolar ratios using successive reduction with hydrazine hydrate (HH) as a reducing agent. The core-shell nanostructures have been further characterized by different characterization techniques. The UV-visible spectroscopy exhibit the respective shift in the band positions suggesting the formation of core-shell nanostructures, which was further confirmed by field emission transmission electron microscopy-high-angle-annular dark field elemental mapping. The effect of metal ion concentration of the core-shell nanostructure on various Gram positive and Gram negative bacteria like Escherichia coli, Staphylococcus aureus, Klebsiella pneumoniae, Pseudomonas aeruginosa and one fungal species Aspergillus fumigatus was observed by performing MIC and MBC/MFC study. Cu-Ag core-shell nanostructures were found to be effective antibacterial agent against all tested Gram-positive and Gram-negative bacteria, whereas Ag-Cu core-shell nanostructures were more efficient against a particular fungal species known as A. fumigatus. The highest value of MIC (75 µg ml-1) for Ag-Cu 0.1M core shell nanostructures (D1) was noted against S. aureus and E. coli whereas the lowest value (20 µg ml-1) was observed with P. aeruginosa. While in case of Cu-Ag 0.1M core shell nanostructures (E1) the highest value of MIC (100 µg ml-1) was noted against S. aureus and P. aeruginosa whereas the lowest value (15 µg ml-1) was observed with A. fumigatus. Also, field effect scanning electron microscope (FESEM) images of untreated and core-shell nanoparticles treated micro-organisms showed that 0.1 M Ag-Cu and 0.1 M Cu-Ag core-shell nanostructure can successfully break the cell wall of the fungi A. fumigatus and bacteria P. aeruginosa, respectively. Thus the present study concludes that, Cu-Ag & Ag-Cu core-shell nanostructures damage the cell structure of micro-organisms and inhibits their growth. Hence, the present Cu-Ag & Ag-Cu core-shell nanostructure acts as good antimicrobial agent against the bacteria and fungi, respectively.