The objective of this paper was to integrate excavation and post-processing of archaeological and osteological contexts and material to enhance the interpretation of these with specific focus on the taphonomical aspects. A method was designed, Virtual Taphonomy, based on the use and integration of image-based 3D modeling techniques into a 3D GIS platform, and tested on a case study. Merging the 3D models and a database directly in the same virtual environment allowed the authors to fully integrate excavation and post-processing in a complex spatial analysis reconnecting contexts excavated on different occasions in the field process. The case study further demonstrated that the method enabled a deeper understanding of the taphonomic agents at work and allowed the construction of a more detailed interpretation of the skeletal remains than possible with more traditional methods. The method also proved to add transparency to the entire research process from field to post-processing and interpretation. Other benefits were the timesaving aspects in documentation, not only in the excavation process but also in post-processing without creating additional costs in material, as the equipment used is available in most archaeological excavations. The authors conclude that this methodology could be employed on a variety of investigations from archaeological to forensic contexts and add significant value in many different respects (for example, detail, objectivity, complexity, time-efficiency) compared to methods currently used.