Invasive fungal infections kill more than 1.7 million and affect over a billion people each year; however, their devastating impact on human health is not widely appreciated and frequently neglected by public health authorities. In 2022, the WHO highlighted the urgent need for efficient diagnostic tests as well as safe and effective new compounds, drugs, and vaccines. Our hypothesis was that the naturally occurring polymer chitosan (CS) could be combined with molecular polyoxometalates (POMs) to produce POM@CS hybrid materials to promote broad-spectrum activity and habilitate synergic effects, which will ultimately help to prevent the appearance of resistances. Here we report the synthesis, characterisation, and antimicrobial activity of POM@CS hydrogels. Spectroscopic (FT-IR & EDS) and electron microscopy (SEM & TEM) techniques revealed the structural composition and morphology of the hybrid materials, whilst dynamic mechanical analysis demonstrated that the mechanical properties of the hydrogels were stable between pH 2 and 10 and were highly resistant to acidic conditions. The POM@CS hydrogels were active against Gram-positive Bacillus subtilis and Gram-negative Escherichia coli bacteria, and proved to completely reduce fungal growth of Aspergillus niger and Cladosporium cladosporioides. Furthermore, the antimicrobial activity of the hydrogels could be enhanced through the inclusion of naturally occurring antimicrobial agents such as eugenol and cinnamaldehyde. Altogether, the development of such surface-active antimicrobial hydrogels pave the way to functional materials that can prevent biofilm formation in health and environmental applications and contribute to reducing the spread of antimicrobial resistance.