Asymmetric Fe-Mn oxide hybrid nanoparticles have been obtained by a seed-mediated thermal decomposition-based synthesis route. The use of benzyl ether as the solvent was found to promote the orientational growth of Mn1-xO onto the iron oxide nanocube seeds yielding mainly dimers and trimers whereas 1-octadecene yields large nanoparticles. HRTEM imaging and HAADF-STEM tomography performed on dimers show that the growth of Mn1-xO occurs preferentially along the edges of iron oxide nanocubes where both oxides share a common crystallographic orientation. Fourier filtering and geometric phase analysis of dimers reveal a lattice mismatch of 5% and a large interfacial strain together with a significant concentration of defects. The saturation magnetization is lower and the coercivity is higher for the Fe-Mn oxide hybrid nanoparticles compared to the iron oxide nanocube seeds.