Although plasmas are used throughout the microelectronics industry for etching, deposition, and cleaning of thin films, control of plasma processes has been a long-standing problem. Because of the nonlinear properties of plasmas, such as the coupling between wave propagation, density profile, and power absorption, plasma reactors are prone to unstable operation, multiple steady states, and hysteresis. We report observation and suppression of an abrupt transition in the operating mode of an electron cyclotron resonance reactor that alters the ion flux to device wafers by more than twofold. While the origin of this mode change is not well understood, we show here that it is strongly correlated with the neutral gas density, which slowly decreases as the reactor temperature increases during a process or from run to run. By measuring the quartz liner temperature and adjusting the pressure to maintain an approximately constant neutral gas density, the mode change can be avoided indefinitely. In a simulated manufacturing process, where the plasma is pulsed on and off, a mode change occurs after several cycles unless the neutral density, instead of the pressure, is controlled.