The Carpathian belt is one of Europe's major metallogenic provinces, where magmatic ore mineralization is associated with the past subduction environment. The upper crust is mapped for the first time in the Northeast Carpathian Volcanic Arc using magnetotelluric data inversion. The obtained 3‐D electrical resistivity model is interpreted in conjunction with geological information and magnetic anomaly data. The model illustrates the deep magmatic plumbing system including kilometer‐scale plutonic bodies at a depth of 2–7 km. The model implies that the transport of magma and fluids in the uppermost crust was controlled by pre‐existing faults and décollement horizons. Present ore mineralization, mined since historical times, can be attributed to an electrically conductive conduit that is mapped from the surface to a depth of about 30 km. It is suggested that this conduit connected a shallow magmatic chamber to a deep source region in the southeast during late Miocene time. An observed northwest deflection of the deep magmatic conduit at a depth of more than 10 km may explain the spatial gap in the distribution of the Miocene volcanic activity along the Eastern Carpathians.