A system and method for treating a substrate in a reaction chamber. A transfer chamber is arranged between a first lock and a second lock, wherein the second lock is provided between the transfer chamber and the reaction chamber. A substrate is transferred into the transfer chamber through the first lock, and the first lock is closed. In a next step, the transfer chamber is flooded with the same gas as in the reaction chamber and the pressure and temperature of the gaseous atmosphere in the transfer chamber is controlled to be the same as in the reaction chamber. Then, the second lock is opened and the substrate is transferred from the transfer chamber into the reaction chamber to treat the substrate. A computer program product for carrying out the above method.