Generation of gold and silver nanoparticles by laser ablation in water without the addition of surfactants is very attractive due to the purity of such nanoparticles. However, such nanoparticles face the problem of long-term stability, which severely limits their applicability. Here, we demonstrate the generation of hybrid gold-silver nanoparticles using the laser ablation of thin-film composites on a glass substrate in water, and compare with the laser fabrication of nanoparticles by using bulk targets of silver and gold. Thin-film method allows the formation of stable hybrid Au–Ag nanoparticles in distilled water without any stabilizers and additional ligands with an opportunity to regulate the nanoparticle composition using different metal ratios, layer order, and thickness of films. The stability and optical properties of the hybrid nanoparticles depend on the used laser pulse energy. This study demonstrates that the thin film method produces nanoparticles with higher stability compared to the bulk target method. These outcomes are encouraging for the creation of better-performing, stable, and clean nanoparticles that can be used in a variety of applications in biomedicine, sensors, integrated circuits, filters, batteries, covid-19 tests, solar cells, dual-energy mammography (DEM), computed tomography (CT), and other components of optical and electronic devices.