Highly fluorescent blue and green-emitting carbon dots have been designed to be integrated into sol-gel processing of hybrid organic-inorganic materials through surface modification with an organosilane, 3-(aminopropyl)triethoxysilane (APTES). The carbon dots have been synthesised using citric acid and urea as precursors; the intense fluorescence exhibited by the nanoparticles, among the highest reported in the scientific literature, has been stabilised against quenching by APTES. When the modification is carried out in an aqueous solution, it leads to the formation of silica around the C-dots and an increase of luminescence, but also to the formation of large clusters which do not allow the deposition of optically transparent films. On the contrary, when the C-dots are modified in ethanol, the APTES improves the stability in the precursor sol even if any passivating thin silica shell does not form. Hybrid films containing APTES-functionalized C-dots are transparent with no traces of C-dots aggregation and show an intense luminescence in the blue and green range.