The building sector is among the sectors with the highest energy use, responsible for 40% of the total energy consumption in the EU. The high energy consumption is partly due to inefficient operation and the delayed detection of faulty systems and components in the buildings, which entails both increased operational costs and CO2-emissions. Thus, building energy performance monitoring and evaluation is key in ensuring a proper building operation and timely detection of anomalies and faults on different levels. This can be implemented through systematic building commissioning, a quality-assuring process aiming to ensure that buildings are operating according to the expected performance. While initial commissioning of newly built buildings has been the norm in the last decades, re-commissioning of deeply retrofitted buildings is generally overlooked despite the potential and positive impacts. In this work, a whole-building EnergyPlus model is developed, calibrated, and employed for the re-commissioning of building components in a Danish health care building that has recently exhibited a deep energy retrofit process on various levels including the installation of new ventilation and cooling units. Both the calibration and the commissioning of these components is performed using data collected from non-invasive clamp-on temperature and power sensors. The commissioning process is performed using a limit checking technique with a predefined threshold, allowing the detection of multiple anomalies during the commissioning period.