This work presents a correlated structural and spectroscopic study on ball-milled MnF₂. The aims are to produce impurity-lean particles through particle-size reduction leading to room-temperature photoluminescence (PL) and to modify the electronic states of the emitting centres. Despite non-radiative centres being still present, the PL quenching temperature was increased nearly 80 K, from 120 to 200 K, following this method. Milled MnF₂ has particle sizes down to several nanometres, and structural changes from the initial α-TiO₂ structure to the α-PbO₂ phase. Milling favours the presence of adsorbed water on the nanoparticle surface. Time-resolved spectroscopy indicates that the nanoparticle PL consists of a significantly inhomogeneous broadened band with respect to the initial MnF₂ PL. The temperature dependence of the lifetime measured at different wavelengths of the emission spectrum indicates the presence of several PL centres, the population of which is controlled by exciton migration and trapping. The widespread occurrence of emitting centres is explained in terms of milling-induced strains, the coexistence of two different structural phases, and the presence of adsorbed water molecules.