In capillary electrophoresis (CE), the temperature inside the capillary is one of the most important parameters. In a concept for Analytical Instrument Qualification (AIQ) of CE systems, the temperature accuracy and stability have to be included. This fact requires an accurate look at the measurement of temperature which is generated by the applied electrical power. The generation of Joule heating is measured on the outside of the capillary using an infrared (IR) thermometer. The thermometer linearity is demonstrated over a wide range of various electrical field strength, buffer systems, and different capillary inner diameters. A slope of 6.3 degrees C m/W was found for the optimal thermometer capillary distance of 8 mm. Furthermore, the temperature measurements are highly precise, depending almost solely on the current variability. The proposed method is compared with three methods calculating the temperature from the conductance, the electroosmotic velocity, or the current. These indirect methods estimate slopes ranging from 7 to 10 degrees C m/W. In addition, the maximal suitable electrical power per unit length is estimated. Joule heating can often be tolerated up to 4 W/m. However, sensitive analytes can already be affected by using more than 1 W/m. In conclusion, the consideration of the temperature is essential for not only Analytical Instrument Qualification, but also certainly useful for method optimisation and method transfer.