At Tell Yunatsite, a prehistoric settlement mound located in the Upper Thracian plain of Bulgaria, stratigraphic relationships between archaeological deposits are incredibly complex. Such complexity then prompted our exploration into developing a new methodology for the documentation of complex stratigraphic relationships. Here, we present the results of a new photogrammetry-assisted methodology ... [Show full abstract] that was developed to compensate for the shortcomings of currently utilized stratigraphic documentation methods, such as the Wheeler-Kenyon box grid and the Harris Matrix. First, using a UAV drone, we produce a high-resolution photogrammetric model of the entire site. Second, with structure from motion photogrammetry, we produce 2.5D models of excavation units in stratigraphic succession. Finally, utilizing GIS and Blender (a 3D computer graphics software application), we digitize the horizontal extents of each archaeological deposit and “fill” the space between their successive surfaces (from top to bottom) until a faithful 3D model of each deposit is generated. These deposit models are then combined and rendered simultaneously to form 3D block models of the excavation units that may, in turn, be cross-sectioned in any direction to view stratigraphic relationships in virtual profile.