The tectonic history of Southern Africa includes Archean formation of cratons, multiple episodes of subduction and rifting and some of the world’s most significant magmatic events. These processes left behind a compositional trail that can be observed in xenoliths and measured by geophysical methods. The abundance of kimberlites in southern Africa makes it an ideal place to test and calibrate mantle geophysical interpretations that can then be applied to less well-constrained regions. Magnetotellurics (MT) is a particularly useful tool for understanding tectonic history because electrical conductivity is sensitive to temperature, bulk composition, accessory minerals and rock fabric. We produced three-dimensional MT models of the southern African mantle taken from the SAMTEX MT dataset, mapped the properties of $\sim36000$ garnet xenocrysts from Group I kimberlites, and compared the results. We found that depleted regions of the mantle are uniformly associated with high electrical resistivities. The conductivity of fertile regions is more complex and depends on the specific tectonic and metasomatic history of the region, including the compositions of metasomatic fluids or melts and the emplacement of metasomatic minerals. The mantle beneath the $\sim 2.05$ Ga Bushveld Complex is highly conductive, probably caused by magmas flowing along a lithospheric weakness zone and precipitating interconnected, conductive accessory minerals such as graphite and sulfides. Kimberlites tend to be emplaced near the edges of the cratons where the mantle below 100 km depth is not highly resistive. Kimberlites avoid strong mantle conductors, suggesting a systematic relationship between their emplacement and mantle composition.