A method and systems for controlling a thrust output of a gas turbine engine are provided. The system includes a first sensor for measuring a first engine operating parameter, a second sensor for measuring a first engine condition parameter, and a processor programmed to determine an expected value of the first engine condition parameter and determine a first variance value using a difference between the expected value of the first engine condition parameter and the measured first engine condition parameter. The processor is further programmed to determine a trim value using the first variance value and a first engine operating parameter demand and to determine a modified operating parameter demand based on the nominal operating parameter demand and the determined trim value. The system also includes a controller coupled to the processor for controlling engine thrust based on the modified demand of the first engine operating parameter.