This paper describes the case study of the damaged church of St. Francesco in the hamlet of Arquata del Tronto (Italy) that was struck by the earthquake in 2016. The municipality commissioned the research to support the preliminary design of the preservation plan. The first digitisation level has been started from the richness of surveying data acquired from static and dynamic terrestrial laser scanning (TLS), and photogrammetry, overcoming challenging constraints due to the scaffolding covering the surfaces. The geometric survey allowed authors to acquire massively geometric and material information supporting the three-dimensional (3D) volume stratigraphic and the creation of the Heritage Building Information Modelling (HBIM). The paper proposes a shift from the Geographic Information System (GIS)-based analysis of the materials toward spatial HBIM management. Building Archaeology is turned into HBIM 3D volume stratigraphy, overcoming the bidimensional (2D) surface mapping, in favour of a 3D understanding of direct and indirect sources. Material mapping is added to HBIM 3D volume stratigraphy, and each stratigraphic unit (SU) has its proprieties. The 3D volume stratigraphic database has been designed to collect the data on the unit detection at three levels (direct sources data collection, indirect data documentation, the relation among the BIM object elements). A common data environment (CDE) has been set up to share the 3D volume informative models that can be accessed, and all the information gathered. The knowledge transfer using the eXtended reality (XR) has been devoted to the citizen and tourist fruition, enhancing the comprehension of difficult concepts like the SUs to support a better critical 3D reconstruction. It includes the phases of construction across time-lapse documentation that validates related information within the building archaeology informative models leaving spaces to the uncertainty and documenting the relationship established so far thanks to the direct and indirect sources. The result obtained is a live digital twin that can be continuously updated, which justifies the costs and time demanding of HBIM despite 2D drawings.Highlights: • 3D survey and scan-to-HBIM process for the creation of a digital twin were oriented to the preliminary design of the preservation plan of the church of St. Francesco in Arquata del Tronto (Italy). • Stratigraphy is investigated and oriented towards a digitisation process to share different levels of knowledge through new forms of digital-sharing such as Common Data Environment (CDE) and cloud-based BIM platform. • eXtended reality (XR) is the final tool to reach new levels of communication and a wider audience characterised by experts in the construction sector and virtual and non-expert tourists.