Mesoporous films obtained by dip-coating, combining polycondensation of silicate species and organization of amphiphilic mesophases, were decorated with iron-based nanoparticles from iron aqueous solution. High-resolution transmission electron microscopy (HR-TEM) images and energy dispersive X-rays spectroscopy (EDS) analysis show that the nanoparticles have diameters between 5 to 10 nm and they are deposited in an ordered sequence exclusively on top of the mesoporous structure. Afterward, by irradiating the material with a hydrogen ion beam, the iron-based compound is functionalized, i.e., its physical-chemical properties are modified. X-ray photoelectron spectroscopy (XPS) showed that the iron oxides and hydroxides are reduced to metallic iron. The deposition of organized iron-based nanoparticles and further ion beam functionalization might open perspectives on the study and fabrication of complex new materials.