Methods and systems for RF pulse reflection reduction are provided herein. In some embodiments, a method includes (a) receiving a process recipe for processing the substrate that includes a plurality of pulsed RF power waveforms from a plurality of RF generators during a first duty cycle, (b) dividing the first duty cycle into a plurality of equal time intervals, (c) for each RF generator, determining a frequency command set for all intervals and send the frequency command set to the RF generator, wherein the frequency command set includes a frequency set point for each of the intervals in the plurality of equal time intervals, and (d) providing a plurality of RF power waveforms from a plurality of RF generators to a process chamber during a first duty cycle according to the frequency command set sent to each RF generator.