A liquid ejecting apparatus including a liquid ejecting portion that ejects a liquid, a liquid supply flow path that supplies the liquid accommodated in a liquid supply source to the liquid ejecting portion, a storage portion that is provided in the liquid supply flow path and that stores the liquid, a pressure mechanism that changes a volume of the storage portion by making pressure act thereon, a liquid filling mechanism that fills the liquid inside the liquid supply source into the liquid supply flow path, and a control portion that fills the liquid into the liquid supply flow path while the volume of the storage portion is, by making pressure act on the flexible portion, made smaller than when the pressure does not act on the flexible portion, and after the filling, ends a state in which the pressure is made to act on the flexible portion.