New hydrogels nanocomposites, based on iminoboronate hydrogels and ZnO nanoparticles (ZnO–NPs), were obtained and characterised in order to develop a new class of disinfectants able to fight the nosocomial infections produced by duodenoscopes investigation procedures. The formation of the imine linkages between chitosan and the aldehyde was demonstrated using NMR and FTIR spectroscopy, while the supramolecular architecture of the developed systems was evaluated via wide-angle X-ray diffraction and polarised optical microscopy. The morphological characterisation of the systems via scanning electron microscopy revealed the highly porous structure of the materials, in which no ZnO agglomeration could be observed, indicating the very fine and homogenous encapsulation of the nanoparticles into the hydrogels. The newly synthetised hydrogels nanocomposites was proven to have synergistic antimicrobial properties, being very efficient as disinfectants against reference strains as:Enterococcus faecalis,Klebsiella pneumoniae, andCandida albicans.