In the coming years, Italy will need to take on a great challenge concerning the digitization of its archaeological and architectural heritage, one of the richest and most problematic in the world. The aim is to improve the knowledge, conservation, enhancement and accessibility of cultural assets and to make them a resource for national and local development. In this process, the next generation of 3D survey methods (laser scanning and photogrammetry), in combination with diagnostic techniques (spectroscopy analyses) and GIS/BIM (Geographic Information System/Building Information Modeling) solutions, represent a valid support. This work, part of a broader intervention launched by the Municipality of Reggio Calabria for the requalification of some archaeological sites located within its urban and metropolitan area, is focused on the study case of Motta S. Agata. The ancient settlement is located 8 km from Reggio C. in a hilly area difficult to reach and preserves numerous structures in a state of ruin. Among these, two interesting medieval churches are proposed for examination: the church of San Nicola, characterized by five hypogeal funeral crypts, and the chapel of San Basilio, which preserves the traces of a wall painting. A multi-methodological approach including close-range photogrammetry, laser scanning and chemical and thermal analyses was adopted in order to fulfill different tasks: creating a topographic model of the hillfort, mapping the archaeological evidence, digitizing and returning 3D models of the churches, characterizing materials through chemical analyses and monitoring the surfaces with thermal imaging. These combined applications have contributed to reaching the planned goals, i.e., study, conservation, diagnostics, preparation for restoration interventions, development of digital media and dissemination. In this way, a type of interactive museum (made up of virtual tours and informative digital models) has been made available in order to improve the site’s accessibility and inclusivity as well as to test the effect of digitization in attracting tourists and local people toward a place located outside of the usual tourist circuits.