Iron oxide nanoparticles are the basic components of the most promising magnetoresponsive nanoparticle systems for medical (diagnosis and therapy) and bio-related applications. Multi-core iron oxide nanoparticles with a high magnetic moment and well-defined size, shape, and functional coating are designed to fulfill the specific requirements of various biomedical applications, such as contrast agents, heating mediators, drug targeting, or magnetic bioseparation. This review article summarizes recent results in manufacturing multi-core magnetic nanoparticle (MNP) systems emphasizing the synthesis procedures, starting from ferrofluids (with single-core MNPs) as primary materials in various assembly methods to obtain multi-core magnetic particles. The synthesis and functionalization will be followed by the results of advanced physicochemical, structural, and magnetic characterization of multi-core particles, as well as single- and multi-core particle size distribution, morphology, internal structure, agglomerate formation processes, and constant and variable field magnetic properties. The review provides a comprehensive insight into the controlled synthesis and advanced structural and magnetic characterization of multi-core magnetic composites envisaged for nanomedicine and biotechnology.