In this study, detailed microstructural characterisation has been conducted in both as-transformed and hot deformed samples of τ-MnAl-C using transmission electron microscopy. After hot deformation, true twins, dislocations, intrinsic stacking faults and precipitates of Mn3AlC are the main defects in the recrystallised grains. True twins and order twins were distinguished based on differences in their diffraction patterns. A significant fraction of non-recrystallised grains existed, which had microstructures based on combinations of high densities of true twins, dislocations, and deformation bands. The formation of the Mn3AlC precipitates was confirmed and related to the reduction of saturation magnetization and the increase in the Curie temperature of τ-MnAl-C after hot deformation. Antiphase boundaries, which are believed to act as nucleation sites for reverse domains, were not observed in the hot deformed sample.