The application of magnetic nanoparticles requires large amounts of materials of reproducible quality. This work explores the scaled-up synthesis of multi-core iron oxide nanoparticles through the use of thermal decomposition in organic media and kilograms of reagents. To this end, we check the effect of extending the high temperature step from minutes to hours. To address the intrinsic variability of the colloidal crystallization nucleation process, the experiments were repeated and analyzed statistically. Due to the simultaneity of the nuclei growth and agglomeration steps, the nanostructure of the samples produced was a combination of single- and multi-core nanoparticles. The main characteristics of the materials obtained, as well as the reaction yields, were analyzed and compared. As a general rule, yield, particle size, and reproducibility increase when the time at high temperature is prolonged. The samples obtained were ranked in terms of the reproducibility of different structural, colloidal, and magnetic features. The capability of the obtained materials to act as nanoheaters in magnetic hyperthermia was assessed, showing a strong dependence on the crystallite size (calculated by X-ray diffraction), reflecting the nanoparticle volume with a coherent magnetization reversal.