Methods for processing a substrate in a plasma processing, chamber employing a plurality of RF power supplies. The method includes pulsing at a first pulsing frequency a first RF power supply to deliver a first RF signal between a high power state and a low power state. The method further includes switching the RF frequency of a second RF signal output by a second RF power supply between a first predefined RF frequency and a second RF frequency responsive to values of a measurable chamber parameter. The first RF frequency and the second RF frequencies and the thresholds for switching were learned in advance during a learning phase while the first RF signal pulses between the high power state and low power state at a second RF frequency lower than the first RF frequency and while the second RF power supply operates in different modes.