Designing nanoparticles for practical applications requires knowledge and control of how their desired properties relate to their composition and structure. Here, we present a detailed systematic study of mixed iron-manganese oxide nanoparticles, showing that ultrasonication provides the high-energy reaction conditions required for complete atomic level mixing of Fe(III) and Mn(III) when amorphous Fe2O3 nanoparticles are irradiated in the presence of Mn2(CO)10 in ambient atmosphere. X-ray diffraction (XRD) results reveal that the crystal structure of manganese iron mixed oxide nanoparticles changes from spinel to bixbyite with increasing of Mn(III) content. The results of room-temperature magnetization curves are consistent with the XRD patterns and spin density from electron paramagnetic resonance measurements, showing samples converting from superparamagnetic to antiferromagnetic, when the crystal structures of these samples transform from spinel to bixbyite.