Mg1+yCo2-x-yMnxO4 (x = 0, 0.4, 0.5, 0.6; y = 0, 0.04, 0.05, 0.4) was synthesized by the reverse co-precipitation method. Powder X-ray diffraction measurements of the obtained product indicated a spinel structure with the space group Fd3¯m. The compositional homogeneity of the synthesized material was confirmed by scanning transmission electron microscopy-energy dispersive X-ray spectroscopy mapping. Charge and discharge cycle tests showed a discharge capacity higher than 220 mAh g−1 at 90 °C with a cut-off voltage ranging from 0.345 to −1.055 V vs. Ag/Ag+ (2.945–1.545 V vs. Mg/Mg2+). The electronic structure was analyzed by the maximum-entropy method (MEM) based on Rietveld analysis results, which showed that Mg insertion was easier in Mg1+yCo2-x-yMnxO4 than in MgCo2O4, and that the strong covalency of M(16d)-O in Mg1+yCo2-x-yMnxO4 enabled Mg ion conduction at the 8a sites. The strain in MO6 octahedra decreased with increasing Mn substitution. The valence of the transition metals was examined by X-ray absorption fine structure (XAFS) measurements, and the Co and Mn K-edge spectra revealed that Co and Mn are present as trivalent to bivalent and tetravalent to trivalent species, respectively. Both Co and Mn redox processes are considered to contribute to the specific capacity during the first charge-discharge process. Rietveld analysis after charge/discharge confirmed a partly reversible phase transition from the spinel phase to the rock salt type phase.