This study aims to better understand the relationship between the microstructure and magnetic properties of copper ferrite, which is an inverse spinel that present a body-centered tetragonal structure associated with a remarkable Jahn–Teller (JT) effect. For this goal, a sample has been synthesized by the ceramic route from a stoichiometric mixture of high-purity CuO and Fe2O3 powders activated mechanically in a high-energy planetary ball mill. This sample was calcined in air furnace at 1000 ºC for 6 h. As synthetized sample with a cubic structure was divided into two parts and one of them was annealed at 650 ºC for 3 h and slowly cooled to room temperature to obtain a pure tetragonal spinel sample. Furthermore, these two samples were subjected to the same processes of severe plastic deformation by milling for up to 70 h and subsequent annealing at temperatures ranging between 300 and 600 ºC to obtain samples with a mixture of phases in different proportions. For the cubic one, there is no change in its structure due to milling, always remaining 100 % cubic, and the evolution in the saturation magnetization was related to the changes in the density of defects present. On the other hand, copper cations are always found in the octahedral sites of spinel with a tetragonal structure. The small decrease in the degree of inversion to 0.95 induced by milling in this sample is capable of breaking the JT distortion, giving rise to the appearance of a cubic phase. This work demonstrates how the structure, microstructure, defects like stacking faults and deformation twins, and degree of inversion of the different phases are related to changes in magnetic properties.