During Friction Stir Welding (FSW) of complex geometries, the thermal dissipation, induced by geometric features or the surrounding environment, may strongly affect the final weld quality. In order to guarantee a consistent weld quality for different conditions, in-process welding parameter adaptation is needed. This paper studies the effect of thermal dissipation, induced by the backing bar thermal conductivity, on the weld temperature and the temperature controller response to it. A new temperature sensor solution, the Tool-Workpiece Thermocouple (TWT) method, was applied to acquire online temperature measurements during welding. An FSW-robot equipped with temperature control, achieved by rotation speed adaptation, was used. AA7075-T6 lap joints were performed with and without temperature control. The cooling rate during welding was register plus macrographs and tensile tests were assessed. The controller demonstrated a fast response promoting the heat input necessary to maintain the set welding temperature. The results demonstrated that temperature control using the TWT method is suitable to achieve higher joint performance and provides a fast setup of optimal parameters for different environments.