Optically transparent nanoceramics of the composition Mg1-xMnxAl2O4(x = 0.005) with a grain size of 15–40 nm were obtained by thermobaric synthesis in a toroid-type high-pressure chamber in the range P = 4–9 GPa at a temperature of 600 °C. EPR spectroscopy indicates the presence of divalent manganese ions with a characteristic HFS signal. In addition, the signal from F+ centers were registered in the EPR spectrum. It has been established that in the HFS of impurity Mn2+ there is an additional contribution from manganese centers split in the field of rhombic symmetry. Photoluminescence spectroscopy methods revealed the presence of optically active centers based on Mn3+ and Mn4+. With an increase in the synthesis pressure, the conversion of manganese ions localized in octa- and tetra-positions occurs, accompanied by a change in valence. It has been found that some manganese ions with a valence of 2+ can be localized in an octahedral oxygen environment, occupying anti-site positions with reduced point symmetry. The formation of F-type centers, as well as polyvalent manganese centers, was confirmed by the cathodoluminescence method. Changing the synthesis parameters makes it possible to control the ratio of valence manganese ions in the corresponding sites of the spinel crystal lattice, thereby expanding the methodological base of defect nanoengineering.