In this study, the friction stir welding process was employed in lap joining of aluminum alloy 6061–T6 and dual phase 500 steel. The novelty of this study was the focus on the measurement of the intermetallic compounds present in the weld interface. Weld temperature and heat input were recorded and validated against the finite element analysis model using COMSOL Multiphysics^® software. The measurement of the experimental temperature showed a good correlation with the thermal simulation. There was an increase in the intermetallic compound formed in the weld interface as the heat input and weld temperature were increased. Destructive testing showed that the bend test angle was improved with less quantity of the intermetallic produced by controlling the weld temperature. With other parameters kept constant, an increase in weld travel speed reduced the propensity of the intermetallic formation that increased the toughness of the welded joint.