Systems and methods for controlling an engine using feedback from one or more sensors are disclosed. An illustrative control system for controlling a diesel engine may include one or more post-combustion sensors adapted to directly sense at least one constituent of exhaust gasses emitted from the exhaust manifold of the engine, and a state observer for estimating the internal state of the diesel engine based on feedback signals received from the post-combustion sensors and from subsequent use of the estimated state in a controller that sends the actuator setpoints. The post-combustion sensors can be configured to directly measure emissions such as oxides of nitrogen (NO.sub.x) and/or particulate matter (PM) within the exhaust stream, and provide such information to a state observer that, in turn, updates an internal dynamical state based on these measurements. In some cases, other sensors such as a torque load sensor, an in-cylinder pressure sensor, and/or a fuel composition sensor can be further used to update the internal state of the state space model, as needed. Using an estimated state from the state observer, a state feedback controller can compute and adjust various actuator setpoints from values that more accurately represent the true state of the system.