We present a new strategy to control the anisotropic diffusion of hydrophilic drugs in lyotropic liquid crystals via the dispersion of magnetic nanoparticles in the mesophase, followed by reorientation of the mesophase domains via an external magnetic field. We select a lipid reverse hexagonal phase doped with magnetic iron oxide nanoparticles and glucose and caffeine as model hybrid mesophase and hydrophilic drugs, respectively. Upon cooling through the disorder-order phase transition of the hexagonal phase and under exposure to an external moderate magnetic field (1.1 T), both the nanoparticles and the hexagonal domains align with their columnar axes along the field direction. As a result, the water nanochannels of the inverted hexagonal domains also align parallel to the field direction, leading to a drug diffusion coefficient parallel to the field direction much larger than what was measured perpendicularly: in the case of glucose, for example, this difference in diffusion coefficients approaches 1 order of magnitude. Drug diffusion of the unaligned reverse hexagonal phase, which consists of randomly distributed domains, shows values in between the parallel and transversal diffusion values. This study shows that modifying the overall alignment of anisotropic mesophases via moderate external fields is a valuable means to control the corresponding transport tensor of the mesophase and demonstrates that the orientation of the domains plays an important role in the diffusion process of foreign hydrophilic molecules.