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In this paper a backstepping controller for a nonlinear, MIMO HVAC system is introduced. Feedback linearization method with introduction of a feedback of states and disturbances is used for the purposes of disturbance decoupling and nonlinear model linearization. The backstepping controller is applied to the linearized model of the system. It is shown that by this method, heat and moisture loads can be compensated, considering them as measurable disturbances. In this way the system can adapt itself to load variations fast and without any offset. Finally the simulation results are brought to show the ability of the method to present a controller with high disturbance decoupling and good tracking properties.