A temperature control system and method controls temperatures of front and back ends of a shift reactor. Front and back end temperature sensors sense temperatures of the front and back ends of the shift reactor and generate front and back end temperature signals. An actuator injects fluid into the front end of the shift reactor. A controller communicates with the front end temperature sensor, the back end temperature sensor and the actuator and controls the temperature of the front end and the back end. The controller includes primary and secondary control loops. The secondary control loop communicates with the back end temperature sensor. The primary control loop communicates with the front end temperature sensor. The secondary control loop generates a temperature setpoint for the primary control loop. The secondary control loop has a slower response time that the primary control loop.