A gas supply subsystem for providing a set of process gases to a substrate processing chamber, the set of process gases being a subset of a plurality of process gases available to the substrate processing chamber. The gas supply subsystem has fewer multi-gas mass flow controllers than the number of available process gases, wherein multiple process gases are multiplexed at the input of one or more of the multi-gas mass flow controllers. Pump-purge may be employed to improve gas switching speed for the multi-gas mass flow controllers.