Iron oxide nanostructures are attractive for a variety of bio-related applications given their wide range of magnetic properties. Here, we report on the study of the magnetophoretic mobility of octapod-shaped nanocrystals, which we relate to stoichiometry, quality and elongation in the 111 direction of these cubic structures. This special morphology combines magnetocrystalline anisotropies, increases shape anisotropy and hinders the formation of an epitaxial wüstite-magnetite interface. As a result, one obtains nanocrystals with large magnetic susceptibility and small coercivity, that is, with optimum characteristics for magnetic guidance, separation, and drug delivery, due to the increased magnetophoretic mobility displayed.