In the current work, we report on synthesizing a series of novel nanocomposite materials obtained by functionalizing the SBA-15 silica matrix with anchored iron phosphonate molecules and following thermal treatment. Obtained results reveal the formation of a unique amorphic layer of Fe-based compounds on the surface of silica walls of SBA-15 channels as a result of the organic groups' decomposition after the moderate thermal treatment. Due to their unique structure, represented in an active Fe-containing amorphous coating spread over a large surface area, these materials are of great interest for their potential applications in fields such as catalysis, adsorption, and non-linear optics. Obtained materials remain amorphous, preserving the SBA-15 mesoporous structure up to the temperatures of approximately 800 °C, after which the partial melting of the silica backbone is observed with simultaneous formation of nanocrystals inside the newly-formed glassy mass. All obtained materials were characterized using such techniques as thermogravimetry, transmission and scanning electron microscopy combined with energy dispersive X-ray spectroscopy mapping, Raman spectroscopy, N2 sorption analysis, X-ray diffraction, X-ray photoelectron spectroscopy, Mössbauer spectroscopy, and SQUID measurements.