In the geomatics field, modelling and georeferencing complex speleological structures are some of the most challenging issues. The use of conventional survey methods (for example, those employing total stations or terrestrial laser scanner) becomes more difficult, especially because of the space constraints and the often critical light conditions. In this work, a flexible and swift methodology to survey an in-progress excavation is presented, through image-based modelling techniques. The proposed approach allows obtaining a reliable and georeferenced three-dimensional model of the underground environments, preserving the integrity of the scene. The 3D model is scaled and georeferenced through three ground control points located just outside the cave, using data acquired by a double-frequency GNSS receiver in static session mode. Further targets were employed to check the deformation of the model inside the cave. The surveys were conducted on two archaeological sites: La Sassa cave and Guattari cave, both located in southern Latium.