The Digital Humanities project Florence As It Was (http://florenceasitwas.wlu.edu) seeks to reconstruct the architectural and decorative appearance of late Medieval and early Modern buildings by combining 3D point cloud models of buildings (i.e. extant structures such as chapels, churches, etc.) with 3D rendered models of artworks that were installed inside them during the fourteenth and fifteenth centuries. This paper documents a novel bifurcated workflow that allows the construction of such integrated 3D models as well as an example case study of a church in Florence, Italy called Orsanmichele (https://3d.wlu.edu/v21/pages/orsanmichele2.html). The key steps worked out in the optimized workflow include: (1) art historical research to identify the original artworks in each building, (2) the use of LiDAR scanners to obtain 3D data (along with associated color information) of the interiors and exteriors of buildings, (3) the use of high resolution photogrammetry of works of art (i.e. paintings and sculptures) which have been removed from those buildings and are now in public collections, (4) the generation of point clouds from the 3D data of the buildings and works of art, (5) the editing and cojoining of a textured polygon model of artworks with a reduced size (using novel algorithms) point cloud model of the buildings in an open-source software tool called Potree so that artworks can be embedded in their original architectural settings, and (6) the annotation of these models with scholarly art historical texts that present viewers immediate access to information, archival evidence, and historical descriptions of these spaces. The integrated point cloud and textured models of buildings and artworks, respectively, plus annotations are then published with Potree. This process has resulted in the development of highly accurate virtual reconstructions of key monuments from the Florentine Middle Ages and Renaissance (like the fourteenth century building of Orsanmichele and the multiple paintings that were once inside it) as they originally appeared. The goal of this project is to create virtual models for scholars and students to explore research questions while providing key information that may assist in generating new projects. Such models represent a significant tool to allow improved teaching of art and architectural history. Furthermore, since the assigned location of some of the historic artworks within these sites are not always firmly known, the virtual model allows users to experiment with potential arrangements of objects in and on the buildings they may have originally decorated.