The present work deals with the preparation of magnetic mesoporous nanocomposites with potential application for cancer treatment. The supramolecular mechanisms that govern the incorporation of γ-Fe2O3nanoparticles into mesoporous silica spheres have been deeply analyzed. The modification of γ-Fe2O3nanoparticles during the encapsulation into mesoporous SiO2 has been studied. The alkaline conditions of these processes lead to an enlargement of maghemite nanoparticles. We hypothesize that this particle enlargement results from Fe3+ cations present in solution. The results presented in this work indicate the importance of the appropriate surface functionalization to incorporate nanosystems into mesoporous silica materials, as well as the modifications that magnetic nanoparticles undergo during the process. Finally, the ability to produce magnetic hyperthermia makes this material a very promising candidate for multifunctional thermoseeds for cancer treatment.