The preparation of tailored nanomaterials able to support cell growth and viability is mandatory for tissue engineering applications. In the present work, silica nanoparticles were prepared by a sol-gel procedure and were then functionalized by condensation of amino groups and by adsorption of silver nanoparticles. Transmission electron microscopy (TEM) imaging was used to establish the morphology and the average dimensions of about 130 nm, which were not affected by the functionalization. The three silica samples were deposited (1 mg/mL) on cover glasses, which were used as a substrate to culture adult human bone marrow-mesenchymal stem cells (hBM-MSCs) and human adipose-derived stem cells (hASCs). The good cell viability over the different silica surfaces was evaluated by monitoring the mitochondrial dehydrogenase activity. The analysis of the morphological parameters (aspect ratio, cell length, and nuclear shape Index) yielded information about the interactions of stem cells with the surface of three different nanoparticles. The data are discussed in terms of chemical properties of the surface of silica nanoparticles.