Herein provided are methods and systems for controlling an engine having a variable geometry mechanism. A pressure ratio between a first pressure at an inlet of the engine and a predetermined reference pressure is determined. An output power for the engine is determined. The output power is adjusted based at least in part on the pressure ratio to obtain a corrected output power. A position control signal for a variable geometry mechanism of the engine is generated based on the corrected output power and the pressure ratio. The position control signal is output to a controller of the engine to control the variable geometry mechanism.