A model-based Fractional Order Proportional-Integral-Derivative (FOPID) control design method is applied to a multivariable greenhouse climate control system. A multivariable transfer function model of the greenhouse system, obtained via model Identification experiment, provides plant’s model information for control design. The fractional controller is tuned using the conventional Biggest Log-modulus Tuning (BLT) method associated with integer order PID controllers. However, unlike the conventional PID case, the controller gains are first computed using internal model control design procedure. This produces preliminary values of controller parameters. The FOPID controller gains are further tuned using a single detuning factor (F) until a biggest log modulus of 2N dB is obtained where N is the number of loops in the MIMO system. Simulation studies, using MATLAB and Simulink, show that good compromise between performance and robustness is achievable for both temperature and humidity regulation in a greenhouse control application.