Methods and apparatus for processing substrates using a multi-chamber processing system (e.g., a cluster tool) that has an increased system throughput and repeatable wafer processing history are provided. In one embodiment a first substrate is transferred from a first position to a second position and then the first substrate is transferred from the second position to a third position using a first robot. A second substrate is transferred from a first position to a second position and then the second substrate is transferred from the second position to a third position using a second robot. The movement of the first and second robots is synchronized so that the movement from the first position to the second position by the first and second robot is performed within a first time interval.