In this paper we report on the successful application of a protein crystallization technique to fabricate a three-dimensionally ordered array of magnetic nanoparticles, i.e. a novel type of metamaterial with unique magnetic properties. We utilize ferritin protein cages for the template-constrained growth of superparamagnetic nanoparticles of magnetite/maghemite Fe3O4-γ-Fe2O3 (magnetoferritin), followed by thorough nanoparticle bioprocessing and purification, and finally by protein crystallization. Protein crystallization is driven by the natural response of proteins to the supersaturation of the electrolyte, which leads to spontaneous nucleation and 3D crystal growth. Within a short period of time (hours to days) we were able to grow functional crystals on the meso-scale, with sizes of the order of tens, up to a few hundred micrometres. We present initial magnetic and Raman spectroscopy characterization results for the obtained 3D arrays of magnetic nanoparticles.