Method for transfer of containers, such as vials (101), between a freeze dryer (1) that is located at a first location and a separate transport vehicle (30) that is mobile with respect to the freeze dryer, wherein the freeze dryer (1) comprises a freeze dryer housing (2) with an access opening (11) towards an inner freeze drying chamber (10) inside the freeze dryer housing (2), multiple shelves (21-24) that are arranged spaced apart above each other inside the freeze dryer chamber (10) and each provided with a horizontally extending first flat supporting surface (25) for supporting the containers, wherein the mobile transport vehicle (30) comprises a mobile undercarriage (31) supporting a storage housing (33) with an access opening (40) towards an inner storage chamber (39), a carrier provided with a second flat supporting surface (58) for supporting the containers inside the storage housing (33), and a container shifter (60) for pushing out containers away from the second flat supporting surface (58) in a pushing out direction parallel to the second flat supporting surface (58).