A particle beam system, such as a multi-beam particle microscope, includes a multi-beam deflection device and a beam stop. The multi-beam deflection device is arranged in the particle-optical beam path downstream of the multi-beam generator and upstream of the beam switch of the particle beam system. The multi-beam deflection device serves collectively blanks a multiplicity of charged individual particle beams. These impinge on a beam stop, which is arranged in the particle-optical beam path level with a site at which a particle beam diameter is reduced or is at a minimum. By way of example, such sites are the cross-over plane of the individual particle beams or an intermediate image plane. Associated methods for operating the particle beam system and associated computer program products are disclosed.