Volcanism in Saudi Arabia includes a historic eruption close to the holy city of Al Madinah. As part of a volcanic hazard assessment of this area, magnetotelluric (MT) data were collected to investigate the structural setting, the distribution of melt within the crust, and the mantle source of volcanism. Interpretation of a new 3‐D resistivity model includes a shallow graben beneath thin lava fields (Harrats), a melt‐free upper crust, and decompression melting in the asthenosphere below thin lithosphere. Within the lower crust the model images elongate conductivity anomalies, one of which was attributed in a previous MT study to melt. The regional MT data, combined with perspective from geology and geophysical modeling, suggest the lower crust is anisotropic with no interconnected melt zones. These divergent interpretations have distinct hazard implications and highlight the importance of large survey aperture and anisotropic modeling to MT studies of volcanic regions. Lower‐crustal anisotropy extends beyond the Harrat, with the most conductive direction oriented N10°E and a factor of 3–5, determined from 2‐D anisotropic inversion, between the most and least conductive directions. The enhanced conductivity is likely due to interconnected grain boundary graphite, while the anisotropy direction reflects either frozen‐in fabric from Neoproterozoic stabilization of the Arabian Shield or modern ductile deformation driven by channelized asthenospheric flow coupled through a thin rigid mantle lid. Asthenospheric melt is interpreted to transect the crust primarily through diking, with limited melt storage and short residence times in the crust.