For providing inline sterile freeze drying of a product containing solid matter and a solvent, such as water, in a plurality of trays accommodated in at least one trolley, a system comprises a filling station having an inlet end and an outlet end, or a docking station, a freeze storage, a freeze dryer unit, an emptying station having an inlet end and an outlet end, or a docking station, a plurality of trays adapted to be accommodated in at least one trolley. A cleaning and sterilizing unit is provided between the outlet end of the emptying station and the inlet end of the filling station.