To investigate the microwave (MW) processing of Fe3O4, for which occurrence of decrystallization has been reported, the micro/nanostructures of MW-heated Fe3O4 powder were observed in this study. The specimens were irradiated by 2.45 GHz MW at the position of magnetic (H)-field maximum in a TE10 single mode applicator. The specimen was heated well above the Curie temperature in H-field. The heated specimen above 1000 °C revealed the glass-like surface with the diminished x-ray diffraction (XRD) peak intensities. They resemble the reported features of decrystallization in an earlier work performed at Penn State University. According to the XRD profiles of the MW-heated specimens, formation of FeO and shift of Fe3O4 peaks to the lower angle with the broadened width were observed. To account for the findings, a model is presented that phase separation occurred into FeO and Fe3O4 resulting in an increased lattice parameter due to the increased oxygen content. This activity is caused by local transport of oxygen in nanoscale. Considering the shape of the main XRD Fe3O4 peak with a shoulder and the existence of halo in nanobeam diffraction (NBD), amorphous phase areas exist. As a result of transmission electron microscopy observation, it was shown that they were in nanoscaled localized regions, and it was not confirmed that the glass-like morphologies (or decrystallized morphologies) are totally amorphous. The observed micro/nanostructures and mechanism of the amorphous phase formation were discussed considering the Fe-O phase diagram.