Aspects of the present disclosure describe techniques for fast stabilization of multiple controller beams with continuous integrating filter. For example, a method is described for intensity stabilization of laser beams (e.g., ion controller beams) in a trapped ion system, where the method includes applying a linear array of laser beams to respective ions in a linear array of ions in a trap, performing, in response to the laser beams being applied, parallel measurements on the ions, the parallel measurements including multiple, separate measurements on each of the ions to identify fluctuations in intensity in the respective laser beams at each ion, and adjusting the intensity of one or more of the laser beams in response to fluctuations being identified from the parallel measurements. A corresponding system for intensity stabilization of laser beams in a trapped ion system is also described.