The development of modern technology is also towards the use of microorganisms as microfactories of the biomaterials with unique properties. Combining the original properties of biosilica extracted from diatoms (microalgae) together with immobilised silver and cerium in nanoparticle forms, allowed to obtain a modern composite material with antibacterial activity. The synthesised composites contained heteroepitaxially growing Ag/AgCl/CeO2 complex nanoparticles were studied using a different types of instrumental analysis. SEM-EDX and XRD analysis allowed the qualitative and quantitative determination of the elements present and their forms in the composites. TEM analysis allowed to information about the shape, size and structure specificity of the created nanoparticles. The possible mechanism of nanoparticles formation was suggested. Antibacterial properties of synthesised composites were characterised using a minimum inhibitory concentration test on six selected bacterial strains. Diatomaceous biosilica containing heteroepitaxially growing silver chloride, metallic silver, and cerium (IV) oxide nanoparticles have been prepared for the first time. The proposed method for synthesising composites did not use toxic reagents, making it environmentally friendly.