Chitosan based hydrogels are a class of cross-linked materials intensely studied for their biomedical, industrial and environmental application, but their biomedical use is limited because of the toxicity of different organic crosslinkers. To overcome this disadvantage, a new strategy to produce supramolecular chitosan hydrogels using low molecular weight compounds able to form covalent linkages and H-bonds to give a dual crosslinking is proposed. For this purpose we used 2-formylphenylboronic acid, which brings the advantage of imine stabilization via iminoboronate formation and potential antifungal activity due to the presence of boric acid residue. FTIR and NMR spectroscopy indicated that the gelling process took place by chemo-physical crosslinking forming a dual iminoboronate-chitosan network. Further, X-ray diffraction demonstrated a three-dimensional nanostructuring of the iminoboronate network with consequences on the micrometer-scale morphology and on the improvement of mechanical properties, as demonstrated by SEM and rheological investigation. The hydrogels proved strong antifungal activity against Candida planktonic yeasts and biofilms, promising to be a friendly treatment of the recurrent vulvovaginitis infections.