Optically transparent Mg1−xMnxAl2O4 (x = 0.005; 0.00005) nanoceramics were obtained by thermobaric synthesis. Varying the parameters of thermobaric synthesis leads to a controlled modification of crystallographic parameters, such as the lattice constant, the region of coherent scattering, and residual strain. It is shown that as a result of thermobaric pressing, intrinsic and impurity structural defects are formed, the concentration of which depends on the P-T parameters. Two stages of thermobaric synthesis were found, differing by both crystallographic and optical parameters. In optically transparent nanoceramics, a correlation between the residual strain and a scattering coefficient associated with localization of impurity manganese ions in anti-site positions of spinel was found. Thermobaric synthesis of optical nanoceramics can be used as a method of compressing nanosized objects in an optical spinel matrix while maintaining such objects in a metastable state.