A system for handling containers in a freight compartment of a vehicle has a stowage device with a frame in which there are formed devices for receiving containers, at least one robot arm, each with a base a handling tool, a guide device mountable on the frame, and a control unit. The robot arm uses the handling tool to receive and move containers to and from the devices. The guide device moves the robot arm along at least one guide axis. On demand, the control unit actuates the robot arm(s) and the guide device such that a container is received from the respective device by the handling tool and is made available at a predetermined transfer position outside the frame, or such that a container is received by the handling tool at the transfer position and inserted into a device.