A control system of a gas turbine engine is provided. The engine has a fuel flow metering valve which regulates a fuel flow to the engine, and one or more variable geometry components which are movable between different set points to vary an operating configuration of the engine. The control system has an engine fuel control sub-system which provides a fuel flow demand signal for controlling the fuel flow metering valve. The control system further has a variable geometry control sub-system which determines current set points to be adopted by the variable geometry components given the current engine operating condition in order to comply with one or more engine constraints. The control system further has an optimiser that receives the current set points and determines adjusted values of the set points which optimise, while complying with the engine constraints, an objective function modelling a performance characteristic of the engine, the objective function adapting to change in engine performance with time. The control system further has a feedback loop in which the adjusted values of the set points thus-determined are sent to the variable geometry control sub-system to vary the current set points.