A method for generating stabilized particle acceleration by a radio-frequency (RF) accelerator is described, comprising operating the accelerator in a warm-up mode during a warm-up time period, without injecting charged particles or without accelerating injected charged particles, and operating the accelerator in a beam-on mode during a beam-on time period after the warm-up time period, to accelerate charged particles injected by the charged particle source. Automatic frequency control to match an expected frequency of the accelerator during the beam-on time period, prior to the start of the beam-on time period, for stability, is also described.