A charged-particle beam (CPB) is aligned to a primary axis of a CPB microscope by determining a first beam deflection drive to a beam deflector for directing the CPB passing a reference location displaced from the primary axis. The beam deflector is provided with a second beam deflection drive during the working mode of the CPB microscope to propagate the beam along the primary axis. The second beam deflection drive is determined based on the first beam deflection drive.