Rutin, the glycoside of quercetin, could be used in topical preparations because of its antioxidant and radical scavenging properties, but its employ in cosmetic and pharmaceutical products is limited by poor physico-chemical stability. These issues were addressed by preparing, characterizing and testing rutin inclusion complexes with MCM-41 mesoporous silica. The effect of surface functionalization with aminopropyl groups (NH2-MCM-41) on the molecules properties was studied. The organic/inorganic interaction was confirmed by XRD, TGA, gas-volumetric analysis (BET) and FTIR spectroscopy. In particular, the high inclusion of rutin in the pores of NH2-MCM-41 was confirmed by many techniques, while FTIR allowed to analyze with great detail the molecular interaction with the inorganic and hybrid surface. Rutin was stabilized against UV degradation, mostly by its inclusion in NH2-MCM-41. Ex vivo studies showed a greater accumulation in porcine skin in the case of rutin complexed with NH2-MCM-41. Not only antioxidant properties of rutin were maintained after immobilization but, with aminopropyl silica, the metal-chelating activity increased noticeably. The immobilization of rutin in aminopropyl silica resulted in better performance in terms of activity and photostability, suggesting the importance of functionalization in stabilizing organic molecules within silica pores.