The Heritage Building Information Modeling (HBIM) is a consistent approach to support the multidisciplinary process of knowledge, conservation, and valorization of the historical building heritage, exploiting the combination of advanced 3D modelling and heterogeneous informative data. In the present paper, a highly customized HBIM workflow is developed for the enhancement and conservation of the byzantine Stylite Tower in the Jordan archaeological site of Umm ar-Rasas. The case study is considered a benchmark to test the effectiveness and the scalability of the proposed methodology for the broader set of ancient structures located in archaeological sites. The proposed HBIM process has a dual aim: the organization of heterogeneous and fragmented sources concerning the history and the actual state maintenance of the Tower and the development of a flexible tool to perform fast qualitative and quantitative analysis oriented towards conservation and management projects. The small scale of the structure and an innovative semi-automatic modelling process based on visual coding allowed for a stone-by-stone segmentation of the Tower. The model procedure is based on an information management workflow based on CIDOC-CRM ontology and the interchange format Industry Foundation Classes to ensure interoperability, developing an open-access interactive visualization of the model of the Tower, embedding organized document sources. The proposed HBIM model can also be a valuable tool for enhanced monument fruition and dissemination activities of the structure.