This work reports on the fabrication of novel type of assemblies bearing magnetic nanoparticles and inorganic shells prepared via a biomimetic route of complex coacervation. Magnetic nanoparticles fabricated under controlled conditions were surface modified with polyacrylic acid (PAA). Subsequently, PAA spontaneously formed spherical assemblies in contact with certain ions, such as Ca2+. The stability of these microspheres against environmental alterations such as pH, ionic strength, and dilution was increased through cross-linking. Ethylene diammine (EDA) was used as a cross-linker, which resulted in mechanically stabilized system that does not show sensitivity towards the external pH values. Important parameters for the formation of these coacervates as well as mechanism of formation and cross-linking have been evaluated by FTIR analysis. The cooperative assemblies are still active for further reaction and were used for the growth of an inorganic aluminum oxide shell. SEM analysis of these spheres showed that the structures are hollow with a large interior volume. A biocompatible outer surface combined with the magnetic functionality is very important for the targeted drug delivery devices for biomedical applications.