Two mesostructured silicas with wormhole-like pore arrangement (HMS and MSU-2) were synthesized and evaluated for the first time as carriers for the encapsulation of two bioactive flavonoids (quercetin and naringin). For comparative purposes, a hexagonal mesostructured SBA-15 silica type frequently used as encapsulating support was also prepared and tested. All the materials were characterized before and after the loading with the analytes. Different silica/analyte ratios were evaluated to determine the loading and encapsulation kinetics of the different materials. Both flavonoids were successfully loaded inside the pores of the three silicas. The quercetin loading capacity of HMS was higher than SBA-15 and MSU-2 silicas, whereas for naringin SBA-15 and MSU-2 were slightly more effective. These differences could be attributed to the molecular size of the analytes and the textural properties of the different materials. Nevertheless, HMS was the silica that enabled to release the highest amount of both analytes. Thus, it could be considered a suitable carrier of these flavonoids and an alternative to other materials such as SBA-15. Moreover, the release process was performed under controlled conditions (pH 2.0 and 7.4) to simulate digestive conditions. Quercetin was delivered faster and more efficiently from the encapsulated at pH 2.0, whereas no differences were observed for naringin at both pHs. Finally, the antioxidant activity of the resulting encapsulates was determined. The results obtained suggested the potential use of wormhole-like mesostructured silicas as carriers to enhance the stability and bioavailability of flavonoids, so they can be used in future food and biomedical applications.