Previous research within friction stir welding (FSW) has demonstrated that online control of welding parameters can improve the mechanical properties and is necessary for certain applications to guarantee a consistent weld quality. One approach to control the process is by adapting the heat input to maintain a stable welding temperature, within the specified operating boundaries. This requires accurate in-process temperature measurements. This paper presents a novel method to measure the temperature at the interface of the FSW tool and workpiece. The method is based on the thermoelectric effect between dissimilar materials. The measurements are compared to thermocouple measurements and to a physical model and show good correspondence to each other. Experiments demonstrate that the method can quickly detect temperature variations, due to geometrical variations of the workpiece or due to parameter changes. This allows use of the method for online control of robotic FSW.