In active continental rifts, asthenospheric upwelling and crustal thinning result in the ascent of melt through the crust to the surface. In the Main Ethiopian Rift (MER) most volcanic activity is located in magmatic segments in the rift centre, but there are also areas of significant off-axis magmatism. Imaging the deeper parts of magmatic plumbing systems is possible with several geophysical techniques including magnetotellurics (MT). We collected MT data at 67 sites and derived a three-dimensional inversion model of the electrical conductivity in the Central Main Ethiopian Rift, testing inversion parameters and model feature robustness. High conductivity indicating the presence of melt and potential pathways in the upper crust (above 5 km depth) is found in only a few places. In contrast at mid crustal level below 15 km depth, higher conductivity values associated with partial melt is pervasive along the north-western part of the rift. Using mixing models and geochemical estimates of melt conductivities we derive melt content estimates for the middle to lower crust. We compare the conductivity model with regional shear wave tomography results. In the lower crust there are lower shear wave velocities coinciding with higher conductivities, indicating the presence of partial melt. Furthermore, there is a high velocity anomaly in the upper crust (5 km) under Aluto volcano, where MT images a resistive body. Both observations are consistent with an older cooled magma body.