A method for dynamically controlling a multiple input, multiple output (MIMO) system having multiple input and output constraints, the method comprising. In an exemplary embodiment, the method includes configuring a MIMO tracking controller to implement closed loop tracking of multiple control reference inputs of the system, in the absence of input and output constraints, and configuring a MIMO constraint controller to enforce the input and output constraints of the MIMO system by generating a reference modification applied to the multiple control reference inputs.