Supraparticles (SPs) consisting of superparamagnetic iron oxide nanoparticles (SPIONs) are of great interest for biomedical applications and magnetic separation. To enable their functionalization with biomolecules and to improve their stability in aqueous dispersion, polymer shells are grown on the SPs' surface. Robust polymer encapsulation and functionalization is achieved via atom transfer radical polymerization (ATRP), improving the reaction control compared to free radical polymerizations. This study presents the emulsion-based assembly of differently sized cubic SPIONs (12-30 nm) into SPs with diameters ranging from ∼200 to ∼400 nm using dodecyltrimethylammonium bromide (DTAB) as the surfactant. The successful formation of well-defined spherical SPs depends upon the method used for mixing the SPION dispersion with the surfactant solution and requires the precise adjustment of the surfactant concentration. After purification, the SPs are encapsulated by growing surface-grafted polystyrene shells via activators generated by electron transfer (AGET) ATRP. The polymer shell can be decorated with functional groups (azide and carboxylate) using monomer blends for the polymerization reaction. When the amount of the monomer is varied, the shell thickness as well as the interparticle distances between the encapsulated SPIONs can be tuned with nanometer-scale precision. Small-angle X-ray scattering (SAXS) reveals that cubic SPIONs form less ordered assemblies within the SPs than spherical SPIONs. As shown by vibrating sample magnetometer measurements, the encapsulated SPs feature the same superparamagnetic behavior as their SPION building blocks. The saturation magnetization ranges between 10 and 30 emu/g and depends upon the nanocubes' size and phase composition.