We report a strong variation of the magnetic properties and of the antiphase boundaries (APBs) density of Fe3O4(001) epitaxial thin films grown on thin Fe(001) and Cr(001) buffer layers on a MgO(001) substrate in comparison with similar magnetite films grown directly on MgO(001). The magnetization of the Fe/Fe3O4 and Cr/Fe3O4 bilayers presents a more squared hysteresis loop and reach saturation at much lower magnetic field (∼10–15 kOe) than the Fe3O4 thin films of same thickness, which hardly saturate at 70 kOe. The magnetization of the magnetite layers has been estimated on both the Fe- and Cr-based samples and a value close to that of the bulk Fe3O4 has been obtained, which points to the magnetic saturation of the Fe3O4 layer induced by the metallic buffers. Transmission electron microscopy has been used to investigate the possible structural origin of this phenomenon studying the APB network of Fe3O4 in the three types of samples. The calculation of the average domain size reveals that the APB density in the bilayers is substantially reduced in comparison with their counterparts without buffer. The domain sizes obtained in Fe and Cr samples are similar, which points to a structural origin probably due to the strain caused by the lattice misfit between the buffers and the magnetite. A lower APB density statistically reduces the influence of the anti- ferromagnetic interactions existing across some of the boundaries, achieving the saturation of the Fe3O4 layer at much lower magnetic fields.