Nowadays the most common gastrointestinal related gram‐negative H. pylori and E. coli pathogen bacteria that are considered to be the main causes for the development of various gastric diseases and bloodstream infections are rapidly developing resistance against the standard antibiotics, commonly used in the clinical practices. One of the alternative high potential approaches for solving problems of bacterial resistance includes applications of silver‐based materials and silver nanoparticles (AgNPs). In the present study two types of amine‐ and triazol‐ functional polyorganosilsesquioxane nanocomposite sorbent hydrogels with narrowly dispersed AgNPs were developed. In vitro antibacterial activity and cytotoxicity tests showed concentration‐ and time‐dependent activity of the prepared nanocomposites against gram‐negative E. coli and H. pylori bacteria and a reduced cytotoxicity towards Caco‐2 human colon epithelial cells. Molecular structures and chemical compositions of the synthesized composites elucidated with transmission and scanning electron microscopy and UV‐Vis spectroscopy revealed spherical and narrowly dispersed along the polymer matrices AgNPs with average sizes of 3–5 nm. It was estimated that the chemical composition and particularly the zeta‐potentials values that were found to be dependent on the molecular structures of the synthesized nanocomposites had a high influence on the AgNPs antibacterial activity and cytoxicity profiles.