Single-atom catalysts are acknowledged for their superior efficiency compared to nanoparticles or clusters, primarily because of the enhanced accessibility of the catalytic center. Essential parameters for assessing their performance are the metal loading degree and oxidation state of the individual catalytic sites. This is particularly the case in Fe-based Fenton-like reaction, in which both Fe2+ and Fe3+ are active but react with significantly different catalytic rates. While the elemental metal loading can be easily assessed by elemental analysis, the determination of the oxidation degree is more challenging. To do so, we designed single Fe-based meso-macroporous silica materials as catalysts for the degradation of methylene blue, an organic dye serving as a well-known model for the degradation of organic pollutants in wastewater. The silica materials were successfully synthesized by a sol–gel process through a combined templating mechanism with micelles and solid lipid nanoparticles of Fe-based surfactants. Magnetic measurements have revealed that half of the iron centers are in the Fe2+ state. The tracking of the Fenton like reaction through magnetic measurements agrees with the contribution of Fe2+ in the catalytic process. The magnetic response emerges as a valuable tool for quantifying and characterizing individual catalytic centers.