The magma plumbing system of Merapi volcano is a key for understanding its eruptive activity and thus has received scientific interest for a considerable time. First detailed attempts to resolve the volcano's internal structure and alleged magma reservoir were carried out at the beginning of the 1990s and included measurements of electrical conductivity, material density, seismic velocities as well as geodetic parameters and surface deformations. Major questions addressed were: (1) where do the fluids and magmas come from; (2) what are the magma ascent paths; (3) where are fluids and partial melts stored; and (4) what is the size and geometry of the magma and fluid reservoirs and the volcanic conduit? Here we review experiments and findings we made during various stages of investigation at Merapi volcano, and also discuss selected projects by other teams and projects. By using seismic methods different crustal zones could be identified with low-velocity values and high Vp/Vs ratios, which can be explained as fluid- and melt-hosting zones. Large-scale joint seismic experiments (MERAPI, MERAMEX and DOMERAPI) displayed seismic attenuation and scattering effects seen in the shallow portion of the edifice, revealed the presence of fluid percolation and subvertical fluid-magma transfer zones, and identified crustal and near-Moho magma reservoirs that are being off-centred to the north. The complementary results of these projects contributed to a new structural image and understanding of the deep structure of Merapi over a depth range of more than 100 km. These results are valid not only for Merapi but now serve as an important example of the crustal structure considered for subduction volcanoes elsewhere.