The Main Ethiopian Rift (MER) is accompanied by extensive volcanism and the formation of geothermal systems, both having an imminent impact on lives of millions of local inhabitants. Although previous studies from the region found evidence that asthenospheric upwelling and associated decompression melting provide melt to magmatic mush systems that feed the tectono-volcanic segments in the rift valley, no geophysical model imaged these regional and local scale transcrustal structures within a single comprehensive 3-D model. To fill this gap, we combined regional and local magnetotelluric data sets to obtain the first multi-scale 3-D electrical conductivity model of the central MER. The model clearly images a magma ponding zone with up to 7 vol.% melt at the base of the crust in the western part of the rift, its connection to Aluto volcano via a tectonically controlled transcrustal magmatic mush system and how the melt, stored at shallow crustal depths, supplies heat for Aluto’s geothermal system. Our model provides evidence that different volcano-tectonic lineaments in the rift valley share a common melt source, which has been debated in the past. The presented multi-scale model provides new constraints as well as geologic insights into the melt distribution below the rift and will facilitate future geothermal developments and volcanic hazard assessments in the MER.