The Nasca geoglyphs in the stone desert in southern Peru are part of our world cultural heritage. These remarkable drawings have roused the interest of scientists from different disciplines. Here we report the results of integrated geophysical, petrophysical, mineralogical, and geochemical investigations of the geoglyphs at six test sites in the stone desert around Nasca and Palpa. The geomagnetic measurements revealed clear indications of subsurface structures that differ from the visible surface geoglyphs. The high-resolution geoelectrical images show unexpected resistivity anomalies underneath the geoglyphs down to a depth of about 2 m. Remarkable structures were revealed in both vertical and lateral directions. No evidence was found of geochemical or mineralogical alterations of the natural geogenic materials (desert pavement environment versus geoglyphs). Neither salts nor other mineral materials were used by the Nasca people to alter or prepare the surfaces of geoglyphs. This supports the hypothesis that the Nasca people simply removed stone material down to the natural hard pan horizon to create the geoglyphs.