Methods and systems for controlling a diesel engine using a combined fuel and air-side controller are disclosed. An illustrative method may include the steps of providing a combined fuel and air-side controller adapted to coordinate both the fuel and air-side control of an engine, sensing one or more parameters, and outputting a fuel profile signal and one or more air-side control signals for controlling at least a part of the fuel-side and at least a part of the air-side of the engine. By centrally coordinating both the fuel and air-side control of the engine, the system can be configured to anticipate future fuel and/or air-side needs of the engine, thus improving system response, performance, and/or emissions.