In the present study, we investigate the combined interaction of mesoporous silica (SiO2) and photocatalytic titanium dioxide (TiO2) nanoparticles with lipid membranes, using neutron reflectometry (NR), cryo-transmission electron microscopy (cryo-TEM), fluorescence oxidation assays, dynamic light scattering (DLS), and zeta-potential measurements. Based on DLS, TiO2 nanoparticles were found to display strongly improved colloidal stability at physiological pH of skin (pH 5.4) after incorporation into either smooth or spiky ("virus-like") mesoporous silica nanoparticles at low pH, the latter demonstrated by cryo-TEM. At the same time, such matrix-bound TiO2 nanoparticles retain their ability to destabilize anionic bacteria-mimicking lipid membranes under UV-illumination. Quenching experiments indicated both hydroxyl and superoxide radicals to contribute to this, while NR showed that free TiO2 nanoparticles and TiO2 loaded into mesoporous silica nanoparticles induced comparable effects on supported lipid membranes, including membrane thinning, lipid removal, and formation of a partially disordered outer membrane leaflet. By comparing effects for smooth and virus-like mesoporous nanoparticles as matrices for TiO2 nanoparticles, the interplay between photocatalytic and direct membrane binding effects were elucidated. Taken together, the study outlines how photocatalytic nanoparticles can be readily incorporated into mesoporous silica nanoparticles for increased colloidal stability and yet retain most of their capacity for photocatalytic destabilization of lipid membranes, and with maintained mechanisms for oxidative membrane destabilization. As such, the study provides new mechanistic information to the widely employed, but poorly understood, practice of loading photocatalytic nanomaterials onto/into matrix materials for increased performance.