The Barberton Greenstone Belt (BGB) in South Africa is one of the few well-preserved, albeit deformed and complex volcano-sedimentary remnants from the Paleoarchean, and thus an excellent locality to study the formation and evolution of the early Earth’s crust. Due to the significant amounts of resources, especially gold in shear zones, the BGB has been extensively studied by geologists for almost 100 years. While the surface geology is well known, only a few geophysical studies have been conducted to investigate the deeper architecture of the BGB and its granitoid surroundings. Here we describe the results of a Magnetotelluric (MT) survey that was conducted over two field seasons to image the subsurface electrical conductivity distribution of geological units of the southern BGB, and to locate dykes, faults and shear zones that are imprints of subsequent tectonic processes. Specifically, mineralization along the shear zones is predicted to reveal high electrical conductivities, in contrast with highly resistive adjacent mafic to ultramafic rocks. The MT station layout of our survey was planned to allow for 2D and 3D interpretation, although it was expected that the 2D inversion models might not be adequate to reveal the expected complex subsurface geology of the BGB and its surrounding region. However, both 2D and 3D inversion results show electrically conductive structures that appear to correlate well with surface traces of known fault zones such as the Inyoka-Saddleback fault system. High resolution 2D conductivity images along selected profiles suggest that some faults might continue further south into the granitoids of the Mpuluzi batholith, implying that the batholith was emplaced along faults (Inyoka-Saddleback fault system and/or Komati Fault), or that a younger fault cuts across the pre-existing batholith. This is contrasted by 3D models that reveal deep-reaching (>10 km) resistive structures beneath the intrusive bodies within the BGB and surrounding batholiths. These results suggest that the granitoids are not disrupted by shear zones, and may imply that episodes of predominant magmatic emplacement have affected the BGB in large parts. A network of conductive faults, especially in the central part of the BGB, suggests that tectonic processes along shear planes have also shaped the BGB, and may have provided pathways for fluids creating zones of gold mineralization.