In one aspect, a method for unloading harvested crop from an agricultural harvester may include monitoring a quantity of the harvested crop discharged from the harvester based on sensor data indicative of the quantity of the harvested crop discharged from the harvester. The method may further include controlling an operation of a flow control device of the harvester to halt transfer of the harvested crop from a crop tank of the harvester to a crop discharge system of the harvester when a first quantity of the harvested crop has been discharged from the harvester. Additionally, the method may include continuing to control an operation of the crop discharge system after halting further transfer of the harvested crop from the crop tank to the crop discharge system to convey any remaining harvested crop contained within the crop discharge system to the discharge location.