Polyoxometalates (POMs) were used, together with chitosan (CS), to obtain hybrid nanoaggregates. Three representative POMs were efficiently assembled into nanoparticles of few hundred nm diameter, featuring entangled ribbons substructure. In order to establish suitable preparation and stability conditions, the assemblies were characterized in solution by UV–Vis spectroscopy, dynamic light scattering and ζ-potential. The nanoparticles were tested against E. coli (106 CFU/ml) in aqueous solution, showing a synergic activity of the heteropolyacid H5PMo10V2O40 and CS. For such components, a highly porous and antibacterial film was obtained upon lyophilisation of the colloidal mixture.