A system is provided for controlling an air handling system for an internal combustion engine. A dual-stage turbocharger includes a high-pressure compressor and variable geometry turbine combination fluidly coupled to a low-pressure compressor and variable geometry turbine combination. A control circuit includes a memory having instructions stored therein that are executable by the control circuit to determine a target low-pressure compressor ratio, a target high-pressure compressor ratio, a target high-pressure compressor inlet temperature and a target high-pressure compressor inlet pressure as a function of a target outlet pressure of the high-pressure compressor and a temperature, a pressure and a target flow rate of air entering the air inlet of the low-pressure compressor, and to control the geometries of the low-pressure and high-pressure turbines as a function of the target low-pressure compressor ratio the target high-pressure compressor ratio respectively.