The main objective of any bioenvironmental controller is to create favourable bioenvironmental conditions around the living-system. In industrial incubation practice of chicken embryo, it is sometimes difficult to fill large incubators with uniform eggs, which leads to suboptimal results. The ideal incubation solution is a machine that is capable of coping with all sorts of variabilities in eggs. This can be realised in practice by creating different zones of different environmental conditions within the same machine. In the present study, a two-levels controller was designed and implemented to combine both convective and radiative heating to incubate eggs. On the higher level, three model-predictive-control (MPC) constrained controllers were developed to regulate the power applied to nine IR-radiators divided into three zones based on continuous feedback of the eggshell temperatures in each zone. On the lower level, a PID controller was used to maintain the air temperature within an experimental incubator at a fixed level (34 °C) lower than the standard incubation temperature. Four full incubation trials were carried out to test and implement the developed zonal controllers. The implementation results showed that the developed controllers were able to follow the reference trajectory defined for each zone. It was possible to keep the eggshell temperatures within the middle region (zone) different from the sidelong regions (zones) while the air temperature kept constant at 34 °C. The average hatching result (HOF) of the four full incubation trial was 84.0% (±0.5). The developed two-levels control system is a promising technique for demand-based climate controller and to optimizing energy use by using multi-objectives MPCs with constraint on total energy consumption.