A photoelectric conversion apparatus including a plurality of pixels each having: a photoelectric conversion unit; a first charge holding unit; a second charge holding unit; a first gate; and a second gate. In a period when the photoelectric conversion unit is storing charges to be transferred to the first charge holding unit, the potential of the first gate is set to a first potential, and the potential of the second gate is set to a second potential. Both the first potential and the second potential are higher than the potential of the first gate in a period when the charges of the photoelectric conversion unit are transferred to the first charge holding unit and the potential of the second gate in a period when the charges of the photoelectric conversion unit are transferred to the second charge holding unit. The first potential is lower than the second potential.