The influence of structural and dimensional factors on the formation of intrinsic and impurity paramagnetic centers in nanoceramics of aluminum-magnesium spinel is studied. The studied samples (with a grain size of 30 nm) were obtained by thermobaric synthesis. Microcrystalline ceramics and a MgAl2O4 single crystal were used as standards. The single crystal and microceramics contain characteristic Mn2+ paramagnetic centers (hyperfine structure constant (HFS) A = 82 G). In the studied nanoceramic samples in the initial state, both impurity Mn2+ and intrinsic F+ centers are detected. In contrast to nanoceramics, in reference samples centers of the F+ type appear only after irradiation with 130 keV by accelerated electrons. The parameters of the Mn2+ centers in nanoceramics differ significantly from those in microceramics and single crystals. For the Mn2+ center in nanoceramics, the EPR signal is characterized by two anomalous HFS constants (A1 = 91.21 G, A2 = 87.83 G) caused by two varieties of octahedrally coordinated manganese ions (anti-site defects [Mn2+]Al3+). The specific features of the spectral parameters of manganese centers correlate with a decrease in the lattice parameter of MgAl2O4 in the nanostructured state. The observed effects are interpreted based on the proposed charge compensation scheme of [Mn2+]Al3+ with an aluminum anti-site defect and an F+ center.