A method for controlling an operation of a vapor compression system (VCS) determines values of measured outputs of the operation of the VCS that include performance and constrained outputs. The method determines states of the VCS using an estimator model of the VCS defining a relationship between the states of the VCS, control inputs and controlled outputs, such that a difference between outputs predicted using the estimator model and the measured outputs asymptotically approaches zero. The states of the VCS include a main state representing the operation of the VCS and an auxiliary state representing the effect of unknown disturbances on each measured output of the VCS. The control inputs for controlling the operation of the VCS are determined using a prediction model, such that the constrained output satisfies the constraints, and a difference between the performance output and the value of the setpoint asymptotically approaches zero.