Stable suspensions of magnetic nanoparticles (MNPs) with large magnetic moment, m, per particle have tremendous utility in a wide range of biological applications. However, due to the strong magnetic coupling interactions often present in these systems, it is challenging to stabilize individual, high moment, ferro- and ferrimagnetic nanoparticles. A novel approach to encapsulate large, i.e., >100 nm, ferrimagnetic zinc ferrite nanocubes (ZFNCs) with silica after an intermediary layer-by-layer polyelectrolyte deposition step is described in this paper. The seed ZFNCs are uniform in shape and size and have high saturation mass magnetic moment (σs ~100 emu/g, m~4×10−13 emu/particle at 150 Oe). For the MNP system described within, successful silica encapsulation and creation of discrete ZFNCs were realized only after depositing polyelectrolyte multilayers composed of alternating polyallylamine and polystyrene sulfonate. Without the intermediary polyelectrolyte layers, magnetic dipole-dipole interactions led to the formation of linearly chained ZFNCs embedded in a silica matrix. Characterization of particle samples was performed by electron microscopy, energy-dispersive X-ray spectroscopy, infrared spectroscopy, powder X-ray diffraction, dynamic light scattering (hydrodynamic size and ζ-potential), and vibrating sample magnetometry. The results of these characterizations, which were performed after each of the synthetic steps, and synthetic details are presented.