This work describes a microwave synthetic approach for the controlled assembly of α-Fe2O3 nanosystems with defined morphologies, such as hollow nanotubes (NTs), solid nanorods (NRs) and nanodisks (NDs). The morphological control is aided during the crystallization processes by using phosphate anions as key surfactants in solution. Furthermore, the thermal reduction under H2 atmosphere of these NTs, NRs and NDs α-Fe2O3 systems to the correspondent Fe3O4 nanomaterials preserved their initial morphologies. It was observed that the concentration of phosphate anions and volume of solvent had significant impact not only on controlling the shapes and sizes, but also phase composition and stoichiometry of the NTs, NRs and NDs nanoparticles. X-ray Rietveld refinement analysis of the NTs, NRs and NDs systems, after reduction in H2, revealed the presence of zero-valent iron (Fe0) in the final materials, with Fe0 fractions that decreased gradually in % from NTs (∼16%), NRs (∼11%) to NDs (∼0%) upon increasing amount of phosphate anions. Bulk magnetic susceptibility measurements showed clear alterations of the Verwey transition temperatures (TV) and the development of unusual magnetic phenomena, such as magnetic vortex states in NDs, which was subsequently verified by micro-magnetic simulations. From the combination of XRD analysis, bulk magnetic susceptibility and Mössbauer results, we provide herein a detailed mechanistic description of the chemical processes that gated the development of shape-controlled synthesis of NTs, NRs and NDs and give a detailed correlation between specific morphology and magneto-electronic behaviors.