There are provided a microscope apparatus, an observation method, and a microscope apparatus-control program that can more efficiently perform auto-focus control and can shorten an imaging time in a case where a culture vessel is to be scanned by an image forming optical system and the auto-focus control is to be performed at each observation position. Focus information of a culture vessel is detected by a first displacement sensor and a second displacement sensor while a stage is moved to a scanning measurement position from an initial set position, and an auto-focus control unit performs auto-focus control at every observation position on the basis of the focus information in a case where the stage has been moved to the scanning measurement position.