The construction technique of raw earth, which has always been in use in most of the world, has left large monuments or architectural complexes to cultural heritage that need special attention due to the notable vulnerability of the material. A convenient way to deal this threat, besides physical intervention, is by using an information system, such as HBIM (Heritage Building Information Modeling), as a tool for damage assessment and conservation planning. This paper reports on its application in an archaeological setting, in particular, on the Huaca Arco Iris, a religious building of the old city of Chan Chan (Peru), the largest monumental complex in mud on the American continent. The study is part of the bilateral international project between the Consiglio Nazionale delle Ricerche (CNR) and the Consejo Nacional de Ciencia, Tecnología e Innovación Tecnológica (CONCYTEC) in the use of HBIM for the prediction of possible natural or anthropogenic damages to buildings in raw mud. Exploiting the data coming from the direct and indirect analyses, a dedicated ontology is built to guide the management of these data within the information system. The creation of an HBIM system for the archaeological domain, based on the trinomial data–information–knowledge, is presented and validated. Following this approach, a customizable HBIM has been created with the 3D model of the spatial entities of the Huaca. As a result, the semantic relationship of an external wall, taken as the benchmark test of our experiment, with the contained bas-relief and the conservation cover is tested.