We present a comparative study of the morphology and structural as well as magnetic properties of crystalline Fe3O4/NiO bilayers grown on both MgO(001) and SrTiO3(001) substrates by reactive molecular beam epitaxy. These structures were investigated by means of X-ray photoelectron spectroscopy, low-energy electron diffraction, X-ray reflectivity and diffraction, as well as vibrating sample magnetometry. While the lattice mismatch of NiO grown on MgO(001) was only 0.8%, it was exposed to a lateral lattice mismatch of −6.9% if grown on SrTiO3. In the case of Fe3O4, the misfit strain on MgO(001) and SrTiO3(001) amounted to 0.3% and −7.5%, respectively. To clarify the relaxation process of the bilayer system, the film thicknesses of the magnetite and nickel oxide films were varied between 5 and 20 nm. While NiO films were well ordered on both substrates, Fe3O4 films grown on NiO/SrTiO3 exhibited a higher surface roughness as well as lower structural ordering compared to films grown on NiO/MgO. Further, NiO films grew pseudomorphic in the investigated thickness range on MgO substrates without any indication of relaxation, whereas on SrTiO3 the NiO films showed strong strain relaxation. Fe3O4 films also exhibited strong relaxation, even for films of 5 nm thickness on both NiO/MgO and NiO/SrTiO3. The magnetite layers on both substrates showed a fourfold magnetic in-plane anisotropy with magnetic easy axes pointing in 100 directions. The coercive field was strongly enhanced for magnetite grown on NiO/SrTiO3 due to the higher density of structural defects, compared to magnetite grown on NiO/MgO.