Nanowire poly(vinylidene fluoride) (PVDF) polymer membranes activated with Ag and Zn nanoclusters were prepared using the electrospinning method. The structure of membranes was varied by using different polymer concentrations in N,N-dimethylacetamide, electric field strength, and concentration of AgNO3 and ZnCl2 in an electrospinning solution. Materials synthesised were analysed by nitrogen sorption and mercury intrusion porosimetry, X-ray diffraction, scanning electron microscopy with energy dispersive X-ray spectroscopy, thermogravimetry, inductively coupled plasma mass spectroscopy, particle filtration efficiency, and pressure drop methods. The concentration of Ag and Zn nanoclusters in PVDF membranes was established and the influence on nanofibers activity has been discussed. The hydrophobicity of membranes was tested using the wetting (contact) angle measurement method. The human influenza A virus (IAV) A/WSN/1933 (H1N1) strain was used to evaluate the virucidal activity of filtration materials. The virucidal activity increased with Ag nanoclusters concentration in fibres. The most hydrophilic nanofibers with Zn nanoclusters showed very high and practically concentration independent virucidal activity that was two orders of magnitude higher compared to materials activated with Ag nanoclusters.