Nowadays in the Architecture, Engineering, and Construction (AEC) Industry, the construction cost is quantified using 5D BIM software that facilitates and accelerates the cost estimation. However, the cost estimation process, despite using 5D BIM tools, is still heavily reliant on subjective evaluations that are influenced by the judgment of each estimator. Another problem related to the accuracy of the cost estimation is the lack of interoperability and manual input of information, such as rules for extracting quantities. In addition, by using unstructured cost items, the association between these and their geometrical objects is based on the object-attribute relationship. This activity can be time-consuming and prone to errors, leading to ambiguities in evaluations; often, these issues impact the increase in the cost of the subsequent construction stages and legal disputes. The research aims to compare the traditional cost estimation method using Primus, one of the 5D BIM tools present in the construction market for cost estimation and developed by ACCA software, and an innovative one, carried out by the same research group through a code developed with IfcOpenShell. This new method uses structured cost items in IFC, based on a more complex architecture than a simple description in natural language, and defines a cost estimate through the relationship between cost and geometric IFC entities. The results show that this new method can reduce the limitations in the current cost estimation process and that the approach based on relations between entities (new method) results more agile and effective than the approach based on cost assignment via attributes (traditional method). The new method ensures the possibility of automating the association of the cost items to geometric entities querying the cost item based on the information contained in the geometric entities and verifying the plausibility of the link between them and the cost estimate.