Nanoclusters (NCs) composed of nanoparticles (NPs) with different functionalities and having final size in the sub-micrometer range are of great interest for biomedical imaging, drug delivery, sensors, etc. Because some of the functionalities cannot be incorporated into a single NP, e.g., high drug loading combined with strong magnetic properties, here, we present a proof of the concept using an alternative way to combine these properties using different NPs. In particular, starting from polymer and magnetite nanoparticles (MNPs), we produce NCs made out of a statistical distribution of the two components through a process based on aggregation and breakup. The effect of all involved operating parameters, i.e., primary NP size and composition, surfactant type and concentration, and applied hydrodynamic stress on the NC size and internal structure, was systematically investigated using dynamic light scattering (DLS), static light scattering (SLS), and transmission electron microscopy (TEM) analyses. It was found that, by properly tuning the balance between attractive and steric repulsive forces on one side and hydrodynamic stress on the other, NCs as small as 100 nm can be produced. In all cases, the produced NCs have a very compact internal structure characterized by fractal dimension around 2.6. The proposed production strategy to synthesize hetero-NCs composed of mixtures of various primary particles is suitable for the production of multifunctional devices of nanometer size (i.e., approximately 100 nm) for material and biomedical applications.