A clean-in-place filling machine which includes a supply tank connected to a filling nozzle by a filling unit and additionally a flush tank connected to a pump or drain outlet by a valve. A programmable controller operates the machine to fill a container with product from the supply tank via the filling unit and the nozzle, and performs a clean-in-place with a pre-rinse, a wash and a final rinse. The initial rinse is performed by rinsing with a rinsing fluid introduced into the supply tank and exiting the drain outlet via the filling unit, the nozzle, the flush tank and the valve. This is followed by washing with cleaning fluid from the flush tank via the valve, the pump, the supply tank, the filling unit and the nozzle back to the flush tank. This is a closed loop wherein the pressure is provided by the pump and the filling unit is operated to drain the supply tank. The final rinse, rinses with rinsing fluid introduced into the supply tank and exiting the drain outlet via the filling unit, the nozzle, the flush tank and the valve. The pump is disconnected from the supply tank during the final rinse and the valve may be operated to alternately connect the rinsing fluid from the flush tank to the pump to also clean the pump separately.