The assembly of magnetic cores into regular structures may notably influence the properties displayed by a magnetic colloid. Here, key synthesis parameters driving the self‐assembly process capable of organizing colloidal magnetic cores into highly regular and reproducible multi‐core nanoparticles are determined. In addition, a self‐consistent picture that explains the collective magnetic properties exhibited by these complex assemblies is achieved through structural, colloidal, and magnetic means. For this purpose, different strategies to obtain flower‐shaped iron oxide assemblies in the size range 25–100 nm are examined. The routes are based on the partial oxidation of Fe(OH)2, polyol‐mediated synthesis or the reduction of iron acetylacetonate. The nanoparticles are functionalized either with dextran, citric acid, or alternatively embedded in polystyrene and their long‐term stability is assessed. The core size is measured, calculated, and modeled using both structural and magnetic means, while the Debye model and multi‐core extended model are used to study interparticle interactions. This is the first step toward standardized protocols of synthesis and characterization of flower‐shaped nanoparticles.