A multi‐methodological geophysical prospecting was performed in a survey area of the archaeological Phaistos site on the Greek island of Crete, as part of an international research project aimed at investigating the less excavated hills of Phaistos and the underlying plateau. The article provides an assessment of the resolution of the chosen techniques for non‐destructive testing of buried ancient structures in the geological landscape of Phaistos. The magnetic and electromagnetic surveys clearly detected anomalies related to human activity, some of which were subsequently defined in detail by resistivity tomography imaging. In particular, variations of the observed electrical and magnetic parameters perfectly correlate to a wall structure made of calcareous material, which has been brought to light by subsequent excavations that unearthed large sectors of a fortification in a double curtain wall, chronologically consistent with the historical sources about the destruction of Phaistos in 150 bc. Copyright © 2015 John Wiley & Sons, Ltd.