Iron-oxidizing bacteria produce trivalent iron oxides with the controlled crystal phases outside of their cells. Herein we have synthesized iron oxides with controlled oxidation states and crystal phases through a microbial-mineralization-inspired approach in an aqueous solution at low temperature. Trivalent iron oxides, such as lepidocrocite, ferrihydrite, goethite, and hematite, are selectively obtained from an aqueous solution containing divalent iron ions below 90 °C. The presence of a chelating agent facilitates the control of the oxidation states through the ligand-controlled approach because the precipitation of the divalent iron species is inhibited by the complexation between divalent iron ion and a chelating agent. The control of the crystal phases is achieved by the tuning of the synthetic conditions, such as the initial pH, the concentration of a chelating agent, and the reaction temperature. Furthermore, the resultant iron oxides have hierarchically organized structures consisting of nanoscale objects. The microbial-mineralization-inspired approach by using a chelating agent has potentials for the further morphological control of iron oxides and the further application to aqueous-solution syntheses of other metal oxides.