The Late Bronze Age ‘Minoan’ eruption of Santorini, Greece occurred from within an existing caldera. Low-temperature pyroclastic flow emplacement on shallow slopes outside the caldera can only be consistent with the caldera being filled with eruption products that are not preserved. Field observations and seismic reflection surveys suggest that this missing material has been downfaulted. The volume of the caldera infill is estimated as 18–26 km3 dense rock equivalent (DRE), increasing the total of the Minoan eruption deposits to 78–86 km3 DRE and making it the largest known Holocene eruption. This study highlights a general mechanism whereby caldera eruption volumes could be significantly underestimated.