System and method for controlled atmosphere stunning of chickens or turkeys in a batch mode is provided. The disclosed method includes the steps of: loading one or more batches of chickens or turkeys in a stunning chamber and sealably enclosing the stunning chamber to isolate the atmosphere therein. Carbon dioxide is then introduced to the isolated atmosphere in a series of three, four, five or more phases to humanely stun and eventually kill the poultry. The carbon dioxide containing atmosphere is subsequently forcibly exhausted from the stunning chamber and the ranks of cages or modules containing the stunned poultry are advanced to a subsequent processing station such as a tipper or dumping station.