A method for controlling a gas turbine engine having a constrained model based control (CMBC) system. The method including obtaining information about a current and previous states of the engine, updating model data information in the CMBC and a parameter estimation system based on the obtained information, and identifying trends in the data based on the information. The method also includes diagnosing the engine, based on the identified trends, determining at least one of a new constraint, objective, initial condition, model characteristic, prediction horizon, and control horizon for the control system based on the diagnosing step if the diagnosing step identified a fault condition, and adapting the CMBC system based on the at least one new constraint, objective, initial condition, model characteristic, prediction and control horizon. The method further includes generating at least on control command based on the adapting and commanding an actuator based on the control command.