Strategies for controlling the indoor climate in greenhouses are based on a few sensors and actuators in combination with an assumption that climate variables, such as temperature, are uniform throughout the greenhouse. While this is already an improper assumption for conventional greenhouses, it especially does not hold for the new trend of growing crops at multiple layers. In addition, different temperature values are desired at the different layers, which turns out to give an uncontrollability issue with the current set of actuators. To solve this issue, fans are placed at each of the layers and an MPC strategy is employed for controlling this nonlinear MIMO system. A case study further shows that such a control strategy reduces the consumed energy of the greenhouse, while maintaining the desired temperature values.