A methodology has been developed for optimizing building supervisory control strategies, employing building models that incorporate stochastic models of occupant behaviour and serve as the objective function evaluator in a stochastic model predictive control (SMPC) architecture. The SMPC architecture accounts for variability in building performance due to occupant behaviour and is shown to generate a sequence of automatic window opening decisions for a mixed mode building which lead to more robust building performance in the face of occupant window use than a heuristic controller. A set of receding optimization time horizons are described which enable the use of complex building models in simulated SMPC. Results of a case study show that deterministic optimization predicts a 50% increase in building performance, while stochastic optimization leads to a more conservative and more reliable 33% performance improvement, which takes into consideration the impact of occupant behaviour.