An electron microscope comprises: an electron microscope main body including a phase plate that imparts a phase change to an electron wave, a moving mechanism that moves the phase plate, and a detector that acquires an image formed by an electron beam transmitted through a sample; and a control unit that controls the electron microscope main body. The control unit performs a phase plate image acquisition process of acquiring a phase plate image which is an image of the phase plate; an unevenness determination process of determining whether or not the phase plate has unevenness based on the phase plate image; and a moving mechanism control process of moving the phase plate by controlling the moving mechanism when the control unit has determined that the unevenness is present.