This paper presents the development of an accurate digital twin of a 100 m-tall steel truss Atmospheric Observatory tower located at the European Commission (EC)’s Joint Research Centre (JRC) in Italy. The study aims to align material properties and, more important, boundary conditions for the structural model. Wireless accelerometers were used for continuous vibration monitoring at different levels of the tower. Operational Modal Analysis (OMA) techniques were applied to identify the tower’s dynamic parameters, and a Finite Element Method (FEM) model was developed to provide deeper insights into the structural behavior. Model updating techniques were employed to minimize discrepancies between the FEM model and the measured dynamic parameters. The updated numerical model accurately captures the tower’s dynamic behavior, emphasizing the importance of model updating for enhancing the accuracy of digital twins and opening the way to the benefits of digital twins in structural health monitoring and predictive maintenance strategies for complex structures.