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The spread of bacterial infections aggravated by the development of microbial resistance to antibiotics requires the creation of protective antibacterial materials. Nanomaterials with biocides can provide antibacterial and antibiofilm properties against Gram-positive and Gram-negative bacteria. In this work, we synthesized nanocomposites with silver nanoparticles and different polyoxometalates of Keggin-structure (phosphomolybdic, phosphotungstic, and tungstosilicic acids) on eco-friendly nanoclay called halloysite. We found that the nanocomposite containing silver nanoparticles and phosphomolybdic acid deposited on the halloysite possesses the best antibacterial performance of all the obtained composites, having a minimal inhibitory concentration of 0.5 g/L against S. aureus, 0.25 g/L against P. aeruginosa and A. baumannii. This composite reduces the viability of formed biofilms at a concentration of 2.5 g/L.