Historic Building Information Modelling (HBIM) plays a pivotal role in heritage conservation endeavours, offering a robust framework for digitally documenting existing structures and supporting conservation practices. However, HBIM’s efficacy hinges upon the implementation of case-specific approaches to address the requirements and resources of each individual asset and context. This paper defines a flexible and generalisable workflow that encompasses various aspects (i.e., documentation, surveying, vulnerability assessment) to support risk-informed decision making in heritage management tailored to the peculiar conservation needs of the structure. This methodology includes an initial investigation covering historical data collection, metric and condition surveys and non-destructive testing. The second stage includes Finite Element Method (FEM) modelling and structural analysis. All data generated and processed are managed in a multi-purpose HBIM model. The methodology is tested on a relevant case study, namely, the church of Santa Ana in Seville, chosen for its historical significance, intricacy and susceptibility to seismic action. The defined level of detail of the HBIM model is sufficient to inform the structural analysis, being balanced by a more accurate representation of the alterations, through linked orthophotos and a comprehensive list of alphanumerical parameters. This ensures an adequate level of information, optimising the trade-off between model complexity, investigation time requirements, computational burden and reliability in the decision-making process. Field testing and FEM analysis provide valuable insight into the main sources of vulnerability in the building, including the connection between the tower and nave and the slenderness of the columns.