Abstract A small phreatic eruption occurred on April 2018 Iwo‐yama, Kirishima volcanic complex, Japan. We estimated the change in the subsurface resistivity structure before and after the phreatic eruption by repeated magnetotelluric (MT) measurements. A substantial decrease in resistivity was determined in the zone from the surface down to a depth of approximately 200 m whose area corresponded to the extent of surface geothermal activation after the eruption, and is interpreted as the result of mixing of high temperature volcanic fluids into cold shallow groundwater. The low‐resistivity layer, which is interpreted as clay‐rich cap, expanded in a ENE–WSW direction and changed into a more ‘bell‐shaped’ structure that can store high‐temperature fluids more effectively. The uppermost part of the bell‐shaped low‐resistivity zone partly showed an increase in resistivity, which may indicate capping has weakened due to increased temperature or acidification. These results suggest an increased potential for a larger‐scale phreatic eruption.