FTIR and RAMAN spectroscopic methods were used to study the ordering of non-stoichiometric nano-magnesium aluminate spinels (MgOnAl2O3, 0.4 < n < 12) synthesized using a combustion synthesis method. It was established that the degree of structural disorder (i.e., the inversion parameter, i) can be quantified using the intensities of the γ1 and γ5 IR modes or 670 and 723 cm−1 Raman shifts. The results indicated that the as-synthesized materials were heavily disordered and obey earlier conclusions that the defect chemistry of non-stoichiometric spinels is dominated by clusters formed from anti-site defects. Analysis of the temperature dependency of cation distribution in the Mg- and Al-rich samples showed that the spinel phase moved toward equilibrium upon increases in temperature. Where decomposition occurred, the disordered level decreased at temperatures up to 1000 °C. Above this temperature, the order level dropped far below the expected equilibrium value and the γ3 mode (a mode that is characterized for ordered structures, such as a natural spinel) that appears. These findings, together with Raman results of partly decomposed Al-rich samples, support the hypothesis that a MgAl2O4-γ-Al8/3□1/3O4 solid solution comprises of series of complex micro-phases with considerable short-range order.