The Bayankhongor Metal Belt, south-central Mongolia, is a narrow metallogenic belt that extends for more than 100 km. It is an economically significant zone that includes important sources of gold and copper. Unfortunately, the crustal architecture is poorly understood throughout this region, although it is known that crustal architecture strongly influences the development and emplacement of mineral zones. Electrical resistivity is a key physical parameter for mineral exploration that can help to locate mineral deposits and can also determine the crustal structure. We use natural-source magnetotelluric data to generate three-dimensional electrical resistivity models of the shallow crustal structure. The results show that anomalous, low-resistivity (conductive) zones in the upper crust are spatially associated with the surface expressions of known mineral occurences, deposits, and mining projects. We thus infer that the location of the economic mineralization, and its development, is closely linked to the low-resistivity (conductive) signatures and, therefore, to crustal structures due primarily to their influence on fluid flow (for example, structurally enhanced permeability). The low-resistivity (conductive) signatures are possibly related to associated sulfide minerology within the host metamorphic complex and to fault structures and pre-existing weaknesses that facilitated fluid movement and left traces of hydrothermal alteration. Thus the crustal architecture, including crustal boundaries and faults that influence fluid distribution, exerts a first‐order control on the location of the metallogenic belt. By combining our electrical resistivity results with other geological and petrological data we attempt to gain insights into the emplacement and origin of mineral resources.