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Abstract On 29 June 2015, a small phreatic eruption occurred at Hakone volcano, Central Japan, forming several vents in the Owakudani geothermal area on the northern slope of the central cones. Intense earthquake swarm activity and geodetic signals corresponding to the 2015 eruption were also observed within the Hakone caldera. To complement these observations and to characterise the shallow resistivity structure of Hakone caldera, we carried out a three-dimensional inversion of magnetotelluric measurement data acquired at 64 sites across the region. We utilised an unstructured tetrahedral mesh for the inversion code of the edge-based finite element method to account for the steep topography of the region during the inversion process. The main features of the best-fit three-dimensional model are a bell-shaped conductor, the bottom of which shows good agreement with the upper limit of seismicity, beneath the central cones and the Owakudani geothermal area, and several buried bowl-shaped conductive zones beneath the Gora and Kojiri areas. We infer that the main bell-shaped conductor represents a hydrothermally altered zone that acts as a cap or seal to resist the upwelling of volcanic fluids. Enhanced volcanic activity may cause volcanic fluids to pass through the resistive body surrounded by the altered zone and thus promote brittle failure within the resistive body. The overlapping locations of the bowl-shaped conductors, the buried caldera structures and the presence of sodium-chloride-rich hot springs indicate that the conductors represent porous media saturated by high-salinity hot spring waters. The linear clusters of earthquake swarms beneath the Kojiri area may indicate several weak zones that formed due to these structural contrasts.