Many migmatites represent crystallized partially molten crust and therefore record the mechanisms and pathways of orogenic crustal flow. Field and microstructural methods may be insufficient to characterize the planar and linear elements of rock fabric in migmatites due to obscured flow fabrics or protracted deformation. In the Naxos dome (Greece), we test the anisotropy of magnetic susceptibility (AMS) as a tool for recovering mineral fabric symmetry and the kinematic axes of flow in migmatites. Measurements of 155 migmatite samples yield dominantly low values (<300 × 10−6 [SI]) of bulk magnetic susceptibility (Km) consistent with biotite being the dominant carrier of the AMS. Higher values of Km, thermomagnetic, hysteresis, and microstructural data, however, suggest a ferromagnetic contribution from magnetite in a subset of samples (N = 15). Using electron backscatter diffraction (EBSD) analysis, we establish the correspondence of the biotite subfabric with the AMS and structural fabric of the Naxos migmatites. EBSD data from biotite suggests that magnetic lineation in these dominantly paramagnetic migmatites arises from a zone axis orientation of biotite crystals organized about the direction of viscoplastic flow. Over a range of spatial scales, migmatitic foliation and magnetic foliation are well correlated. The magnetic lineation recovered by AMS displays a coherent organization despite the heterogeneous structure and composition of the Naxos migmatites. These data suggest that the apparent complexity of migmatites masks a simpler flow regime controlled by bulk viscoplastic flow. Furthermore, our study demonstrates the utility of the AMS method for studying the dynamics of partially molten orogenic crust.