A system includes a turbocharged engine, sensors, and a controller. The engine includes an engine intake manifold, air intake manifold, a compressor, a first aftercooler device, a throttle that admits cooled compressed air to the engine intake manifold, and cylinders. The sensors determine engine status signals and include a first manifold pressure (MAP) sensor positioned with respect to the first aftercooler device, a second MAP sensor positioned with respect to the engine intake manifold, a mass airflow (MAF) sensor positioned in the air intake manifold, a first manifold temperature (MAT) sensor positioned in the engine intake manifold, and a second MAT sensor positioned between the first aftercooler device and the throttle. The controller executes a method to calculate a cylinder air charge using an oxygen level of post-combustion gasses and the engine status signals, and controls an operation of the engine using the calculated air charge via engine control signals.