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New series of Cu(II) and Mn(II) complexes with Schiff base ligands derived from 2-furylmethylketone (Met), 2-furaldehyde (Fur), and 2-hydroxyacetopheneone (Hyd) have been synthesized in situ on SBA-15-NH2, MCM-48-NH2, and MCM-41-NH2 functionalized supports. The hybrid materials were characterized by X-ray diffraction, nitrogen adsorption–desorption, SEM and TEM microscopy, TG analysis, and AAS, FTIR, EPR, and XPS spectroscopies. Catalytic performances were tested in oxidation with the hydrogen peroxide of cyclohexene and of different aromatic and aliphatic alcohols (benzyl alcohol, 2-methylpropan-1-ol, and 1-buten-3-ol). The catalytic activity was correlated with the type of mesoporous silica support, ligand, and metal–ligand interactions. The best catalytic activity of all tested hybrid materials was obtained in the oxidation of cyclohexene on SBA-15-NH2-MetMn as a heterogeneous catalyst. No leaching was evidenced for Cu and Mn complexes, and the Cu catalysts were more stable due to a more covalent interaction of the metallic ions with the immobilized ligands.