This study implemented a framework of empirical validation of building energy models under uncertainty to a set of controlled experiments that aim to validate multi-zone building and HVAC system models. Energy models were created through iterative acquisitions of information and data and uses measurement data from various types of sensors as both inputs and as observations to validate predictions. Experimental and modeling uncertainties were quantified and propagated accordingly, and probabilistic accuracy metrics were used to evaluate the agreement between model predictions and observations under uncertainty. Sensitivity analysis was performed to identify the most influential uncertainties that will be prioritized to be addressed in the next steps. Current results of two cooling tests show an overall good agreement between predictions and observations on a set of HVAC system outputs despite considerable and influential uncertainty in DX cooling coil COP. Agreements on zone-level responses vary notably among individual rooms, likely because of significant uncertainties in room radiation heat gain and system supply air.