IIn this work, the heating distribution on similar and dissimilar friction stir welded joints in aluminium and magnesium alloys sheets was studied. Friction Stir Welding processes were performed using constant rotational and welding speeds of 1500 rpm and 60 mm/min, respectively. In order to obtain a completely non-intrusive and temperature monitoring measurement technique, a contactless method based on infrared thermography was used to remotely analyse the temperature distribution over the welded area, near the tool during the Friction Stir Welding process. It was observed that the mechanical properties of joints are strictly related to the heat distribution. This system was used both to experimentally evaluate the temperature on the top surface of the joints and as it is able to detect the presence of flow defects with a contactless and non-destructive method, demonstrating the effectiveness of this measuring system as a diagnostic tool for the online quality control of welded joints.