Although multi-stage incubation (mixing the eggs from all stages of incubation in the same machine) is still very common in the poultry industry, it is well known that single stage incubation (having all the eggs in the machine in the same stage of incubation) has advantages for embryo development and quality of the day old chick, due to a better control of the temperature of the eggs. In single stage incubation we can decrease the temperature of the air to compensate for the increase in heat production by the developing embryo, where in multi stage incubation we have to find a sort of an average in temperature, which often means slightly too low at the start and too high at the end.

To control the temperature of the eggs in a multi stage hatchery better, we can split up the incubation process in two different parts, divided over two different machines. In one machine we can place the eggs from start until day 12, and from day 13 onwards we can change the eggs to a second machine with a decreased temperature. As both machines are still operated multi stage, sets of eggs will more or less continuously be added and removed from both machines.

As the extended heat production of the embryo but also the critical phase for overheating is especially in the last part of incubation, this method can help to control the incubation process in multi stage situations better. If we not only decrease the air temperature in the second machine but also stop the turning mechanism and put the trays with eggs horizontal, we can increase the air velocity over the eggs and cool them even more effectively. What the optimal temperature in both machines (one from 0 to 12 days and one from 13 to 18 days) must be should be determined by controlling the egg shell temperature and adjusting the temperatures of the machines accordingly. As every machine has its own specific characteristics, a standard program cannot be given.

This double multi stage setting system cannot be applied in every machine. It must be possible to remove the eggs from the machine in a simple way at 12 days and place them in the second machine. This requires that the eggs are in trolleys that can be moved, so it will not work for fixed rack machines. Also tunnel machines will not be suitable for this system, as it will be difficult or impossible to remove the trolleys without losing capacity. But for machines with trolley setting and a corridor in the machine, it can work quite well although it requires planning and extra labor.

Problem in the second machine (with the eggs from 13 to 18 days) will be that the total heat load is higher than when the eggs in the machines are from 0 to 18 days. This requires adequate cooling of the machines, which sometimes can become a limiting factor.