Disclosed herein are systems and methods for calibration of a charged particle beam microscope, including a source configured to generate a CPB comprising a plurality of charged particles having a known energy; at least one lens; a detector; and a controller. According to various disclosed embodiments, the controller may determine, based on a calibration characteristic, that the CPB microscope requires recalibration. Based on that determination, the controller may operate the source to generate a calibration CPB and configure the at least one lens to act as a charged particle mirror. The controller may receive data from the detector associated with the plurality of charged particles after reflecting off the charged particle mirror. The controller may then analyze the data from the detector and automatically recalibrate the CPB microscope based on calibration characteristics in the data from the detector.