Embodiments for the present application include methods and apparatus for operating a plasma enhanced substrate processing system using dual level pulsed radio frequency (RF) power. More specifically, embodiments of the present disclosure allow for frequency and power tuning in a process chamber using dual level pulsed power by using a tuning controller coupled to a matching network and/or a RF power generator. In one embodiment, a tuning system includes a tuning controller disposed in a tuning system, the tuning controller configured to tune dual level RF pulsing data from a RF power generator, wherein the tuning system is connectable to a plasma processing chamber, and a memory connecting to the tuning controller, wherein the tuning controller is configured to couple to a RF power generator and a matching network disposed in the plasma processing chamber.