Methods and systems are provided for controlling the operation of an air charging system of an internal combustion engine. A plurality of actuators include an electric motor of an air compressor. Output parameters of the air charging system are monitored by a plurality of sensors. An error between each one of the output parameters and a target value thereof is calculated by a processor. The calculated errors are applied to linear controllers that yield virtual inputs. Input parameters for the air charging system are calculated using the virtual inputs. The input parameters affect all of the output parameters. The input parameters are calculated with a non-linear mathematical model of the air charging system, configured such that each one of the virtual inputs is in a linear relation with only one of the output parameters. The actuators are operated using the input parameters.