(Apo)ferritins are cage-shaped proteins which have recently received a great deal of attention because the inner cavity of the protein shell can be used as a size-restricted reaction field for the synthesis of nanomaterials. The biomineralization behavior and inorganic nanoparticle (NP) synthesis mechanism of (apo)ferritin in solution systems have been studied but the mineralization behavior of (apo)ferritin on the substrates has not yet been well studied. Here, we conducted quantitative and kinetic analyses of the mineralization behavior of immobilized (apo)ferritin on a polyelectrolyte multilayer (PEM) using quartz crystal microbalance (QCM), scanning electron microscopy (SEM), and X-ray photoelectron spectroscopy (XPS) techniques. We demonstrated that the (apo)ferritin immobilized on a substrate synthesizes a ferrihydrite core within the confines of the protein cage; similar to a solution dispersed system. In addition, we applied a ferritin/apoferritin blended monolayer to the study of iron mineralization and revealed that biomineralization in this system is spatially selective. It is important to understand the mineralization mechanisms for the synthesis of other functional NPs as this approach has potential for a broad range of magnetic, catalytic, and biomedical sensing applications.