A microwave oven and a method of controlling the same, in which a cooking unit disposed in a cooking cavity is moved from an initial position to a cooking position. In the microwave oven, a magnetron is operated after heaters are moved to respective cooking positions where a rotating unit to move the heaters and the magnetron are operated. Accordingly, microwaves are radiated into the cooking cavity while the heaters are not being moved by the rotating unit, so a generation of heat and sparks resulting from a concentration of the microwaves into spaces between a moving unit including the rotating unit and the cooking unit and between the moving unit and a wall of the cooking cavity is preventable.