Ultra-short pulsed laser ablation of materials in liquid has been demonstrated to be a versatile technique for nanoparticles production. In a previous paper, it has been described, for the first time, how by laser ablation in a liquid system, silver nanoparticles can be loaded onto SBA-15 and MCM-41 supports which show promising catalytic properties for the oxidation of Volatile Organic Compounds (VOCs). The aim of the present research is to demonstrate the formation of stable silver-silica core-shell nanoparticles by direct laser ablation (Ti:Sa; 800 nm; pulse duration: 120 fs; repetition rate: 1 kHz, pulse energy: 3.6 mJ, fluence: 9 J cm − 2) of a Ag target submerged in a static colloidal solution of MCM-41 or SBA-15 silica nanoporous materials. In previous studies, it was discovered that a side and negligible product of the laser ablation process of silver performed in water-silica systems, could be related to the formation of silver-silica core-shell nanoparticles. In order to emphasize this side process some modifications to the laser ablation experimental set-up were performed. Among these, the most important one, in order to favor the production of the core-shell systems, was to keep the liquid silica suspension firm. The laser generated nanomaterials were then analyzed using TEM morphologic characterization. By UV–vis absorption spectra the observed features have been related to components of the colloidal solution as well as to the number of the incident laser pulses. In this manner characterizations on both the process and the resulting suspension have been performed. Significant amount of small sized silver-silica core-shell nanoparticles have been detected in the studied systems. The size distribution, polydispersivity, UV–vis plasmonic bands and stability of the produced silver-silica core-shell nanocomposites have been related to the extent of damage induced in the nanoporous silica structure during the ablation procedure adopted here. In presence of SBA-15 the silver-silica core-shell nanoparticles observed by TEM are smaller and more homogeneously dispersed if compared with the core-shell system obtained when the MCM-41 mesoporous silica was used. The outcomes show that the choice of the mesoporous silica material can affect the silica shell thickness in addition to the Ag NPs size distribution. With this regard, TEM images evidence that in MCM-41 the silver-silica core-shell nanostructures display a silica layer thickness between 1–10 nm; conversely, for SBA-15, the silver-silica core-shell nanoparticles are finely dispersed and the silica shell shows, when present, an average thickness of about 5 nm.