The Aidonia cemetery is an archeological site on the Peleponnese Peninsula in Greece. It was constructed in the Late Bronze Age and consists of chamber tombs dug into rock outcrops. In August 2019, a team of researchers from TU Delft and University of Stavanger acquired detailed 3D scan data of the Aidonia site using a Leica P40 laser scanner. The team scanned the site from 51 scan positions. 29 positions were focusing on the chamber tombs while the other 22 positions sampled the overall cemetery setting. The scans were combined in a common coordinate system providing a point cloud consisting of ~5.9 billion points. Analysis of the point cloud notably provided insight in the architectural setting and current status of the different tombs. The data set in this repository consist of the raw, aligned point cloud. A detailed description of the point cloud data and its application in documenting the status of the Aidoinia cemetery can be found in the corresponding publication, at https://doi.org/10.1016/j.daach.2024.e00319.