Building energy systems often consume approximately 16% more energy than is necessary due to system deviation from the design intent. Identifying the root causes of energy waste in buildings can be challenging largely because energy flows are generally invisible. To help address this challenge, we present a model-based, real-time whole building energy diagnostics and performance monitoring system. The proposed system continuously acquires performance measurements of heating, ventilation and air-conditioning, lighting and plug equipment usage and compare these measurements in real-time to a reference EnergyPlus model that either represents the design intent for the building or has been calibrated to represent acceptable performance. A proof-of-concept demonstration in two real buildings will be presented. The challenges and key learning will be discussed.