Methods and apparatus for calibrating a plurality of gas flows in a substrate processing system are provided herein. In some embodiments, a substrate processing system may include a cluster tool comprising a first process chamber and a second process chamber coupled to a central vacuum transfer chamber; a first flow controller to provide a process gas to the first process chamber; a second flow controller to provide the process gas to the second process chamber; a mass flow verifier to verify a flow rate from each of the first and second flow controllers; a first conduit to selectively couple the first flow controller to the mass flow verifier; and a second conduit to selectively couple the second flow controller to the mass flow verifier.