MCM-41 based catalysts (molar ratio Si/Al = 40) were prepared by a hydrothermal route, modified by ionic exchange with different metals (Cu, Cr, Fe and Zn) and finally calcined at 550 °C. The catalysts were fully characterized by different techniques that confirmed the formation of oxides of the different metals on the surfaces of all materials. Low-angle X-ray diffraction (XRD) analyses showed that calcination resulted in the incorporation of metallic Zn, Fe and Cr in the framework of MCM-41, while in the case of Cu, thin layers of CuO were formed on the surface of MCM-41. The solids obtained were tested in the catalytic wet peroxide oxidation (CWPO) of acetaminophen at different temperatures (25–55 °C). The activity followed the order: Cr/MCM-41 ≥ Fe/MCM-41 > Cu/MCM-41 > Zn/MCM-41. The increase of the reaction temperature improved the performance and activity of Cr/MCM-41 and Fe/MCM-41 catalysts, which achieved complete conversion of acetaminophen in short reaction times (15 min in the case of Cr/MCM-41). Fe/MCM-41 and Cr/MCM-41 were submitted to long-term experiments, being the Fe/MCM-41 catalyst the most stable with a very low metal leaching. The leaching results were better than those previously reported in the literature, confirming the high stability of Fe/MCM-41 catalysts synthesized in this study.