To broaden the application of silver nanoparticles (AgNPs), which are well-known antibacterial agents, they are supported on different substrates to prevent aggregation, increase their surface area and antibacterial efficiency, and to be separated from the system more effectively at the end of treatment. To produce nanocomposites that consist of silver nanoparticles on natural and modified zeolites, silver ions (Ag+) were loaded onto zeolite (natural, Na-modified, H-modified) and then thermally reduced to AgNPs. The effect of the exchangeable cations in zeolite on Ag+ uptake, AgNPs formation, size and morphology was investigated by the TEM, SEM, EDX, XPS, UV-vis, XRD and BET methods. The silver amount in the nanocomposites decreased in the following order Na-modified zeolite > natural zeolite > H-modified zeolite. Microscopic techniques showed formation of AgNPs of 1–14 nm on natural and Na-modified zeolite, while the diameter of metal particles on H-modified zeolite was 12–42 nm. Diffuse reflectance UV-vis and XPS methods revealed the presence of both silver ions and AgNPs in the materials indicating that partial reduction of Ag+ ions took place upon heating at 400 °C in air. Additionally, antibacterial properties of the nanocomposites were tested against Escherichia coli, and it was found that Ag–containing composites originating from the Na-modified zeolite demonstrated the highest activity.