The excavated architecture of the exceptional prehistoric site of Akrotiri on the Greek island of Thera/Santorini is endangered by gradual decay, damage due to accidents, and seismic shocks, being located on an active volcano in an earthquake-prone area. Therefore, in 2013 and 2014 a digital documentation project has been conducted with support of the National Geographic Society in order to generate a detailed digital model of Akrotiri’s architecture using terrestrial laser scanning and image-based modeling. Additionally, non-invasive geophysical prospection has been tested in order to investigate its potential to explore and map yet buried archaeological remains. This article describes the project and the generated results.