An automatic warehouse comprises: a support structure (2) for supporting trays (50) each provided with at least a container cell (51) exhibiting an opening (52); an operating station (3), which is provided with an access opening (4) and is predisposed for receiving at least a tray (50) such that an opening of the container cell (51) faces the access opening (4); the operating station (3) being provided with a cover (5, 6), which cover (5, 6) is mobile on command between an open position, which enables access to the container cell (51) of the tray (50) and a closed position, which prevents access to the container cell (51); a manipulator device (7) to remove and transfer at least a tray (50) from the support structure (2) to the operating station (3), and vice versa.