In this work, magnetic copper ferrite nanoparticles are synthesized by polymer-assisted sol-gel and co-precipitation methods. The obtained purity and particle size reach values of 96 % and 94 nm, respectively. Evident differences in the crystal structure have been found in the synthesized nanoparticles. A tetragonal structure is formed by the sol-gel method, while the cubic form is obtained when the co-precipitation approach is used. This work provides an experimental evidence of the formation of both phases by using the same reactants and thermal conditions, and only modifying the technical procedure. The formation and stability of each phase is analysed by temperature dependent measurements, and the observed crystal structure differences are used to propose a potential fundamental explanation to our observations based on a difference on the cations' distribution and the Jahn-Teller distortion. Moreover, different copper ferrite purity and particle sizes are found when using each of the methods. The spherical shape of the particles and their tendency to sinter forming micrometric clusters are observed by electron microscopy. Finally, the divergence in magnetization between the samples prepared by each method support our argument about the different cations' distribution and open the door to a wide range of different technological applications for these materials.