The Bayankhongor Metal Belt, a metallogenic belt that extends for more than 100 km in central Mongolia, is an economically significant zone that includes sources of gold and copper. Unfortunately, the crustal architecture is poorly understood throughout this region. However, it is known that the crustal structure 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 zones and determine the regional crustal structure. We use natural-source magnetotelluric data to generate three-dimensional electrical resistivity models of the crust. The results show that anomalous, low-resistivity zones in the upper crust are spatially associated with the surface expressions of known mineral occurrences, deposits, and mining projects. We thus infer that the development of the mineralization is closely linked to the low-resistivity signatures and, therefore, to crustal structures, due primarily to their influence on fluid flow. The low-resistivity signatures are possibly related to associated sulfide mineralogy within the host complex and to structures and weaknesses that facilitated fluid movement and contain traces of past hydrothermal alteration. Thus, the crustal architecture, including major crustal boundaries 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.