(1) Background: The onset of inflammation and oxidative stress after biomaterial implantation can lead to complications and prolonged recovery times. To address this, bioactive mesoporous glasses doped with cerium (0, 3.6 and 5.3 mol%) were loaded with three different biomolecules-3-hydroxyflavone, quercetin and morin hydrate-to enhance antioxidant properties while preserving bioactivity. (2) Methods: Elemental analysis, specific surface area determination, spectroscopic techniques, evaluation of antioxidant activity and in vitro bioactivity assessment were performed to characterize mesoporous glass loaded with biomolecules. (3) Results: Biomolecule loading gives values in the range of 0.5-2.0% and 10.3-39.6% for loading content and loading efficiency, respectively. The loading order is quercetin >
morine hydrate >
3-hydroxyflavone, and a cerium percentage of 3.6 seems to be a good compromise. The antioxidant properties evaluated on both solids and solutions in contact with simulated biological fluids improve markedly over loaded glasses, and the most promising results are obtained with quercetin. In the most efficient systems, the bioactivity results were delayed and more evident at longer times (168 h) but were still retained. (4) Conclusions: We obtained new materials still bioactive with improved antioxidant properties that can be proposed for the regeneration of both hard and soft tissues.