Proton beams are a promising alternative to X-rays for therapeutic purposes because they may also destroy cancer cells, but with a greatly reduced damage to healthy tissue. The energy dose in tissue may be concentrated at the tumor site by configuring the beam to position the Bragg Peak proximate the tumor. The longitudinal range of a proton beam in tissue is generally dependent upon the energy of the beam. However, after switching energies, the proton-beam system requires some time for the beam energy to stabilize before it may be used for therapy A proton linear accelerator system is provided for irradiating tissue with an improved beam energy control, configured to provide RF energy from afirst RF energy source during the on-time of the proton beam operating cycle for changing the energy of the proton beam, and to provide RF energy from a second distinct RF energy source during the off-time of the proton beam operating cycle for increasing or maintaining the temperature of the cavity. Each RF source is operated independently, allowing higher RF pulse rates to reach the cavity, supporting a smaller time between proton beam energy pulses. In addition, the peak power requirements for the second RF energy source may, in general, be less than for the second RF energy source, allowing a less costly type to be used for the second source. The use of a first and second RF source may reduce the cavity settling time from minutes to less than 10 seconds.