A system for automatic multivariable calibration of an engine controller. The system may take inputs which include actuator setpoints, sensor measurements, performance requirements, and so forth. There may be an algorithm to compute engine calibration parameters for the controller. Each of the actuators may be separately stepped through to experimentally obtain actuator input and sensor output data. Algorithmic processing of the experimentally obtained data may be performed to calculate parameters of a model of an engine. A model based control design algorithm may then be invoked to obtain the calibration parameters for a controller. The calibrated controller may be tested with real or simulated engine conditions. The performance related to the parameters may be analyzed and determination of the acceptability of the data be made. If not acceptable, the parameters may be reprocessed. If acceptable, the calibration parameters may be downloaded to the engine controller for application and use.