The aim of this research was to investigate the influence of the properties of the base materials and welding speed on the morphology and mechanical behavior of the friction stir welds of three dissimilar aluminum alloys in a T-joint configuration. The base materials were the AA2017-T4, AA5083-H111, and AA6082-T6 alloys in 3 mm-thick sheets. The AA6082-T6 alloy was the stringer, and the other alloys were located either on the advancing or retreating sides of the skin. All the T-joint welds were produced with a constant tool rotation speed but with different welding speeds. The microstructures of the welds were analyzed using optical microscopy, scanning electron microscopy with energy dispersive spectroscopy, and the electron backscatter diffraction technique. The mechanical properties were assessed according to micro-hardness, tensile, and fatigue testing. Good quality welds of the three dissimilar aluminum alloys could be achieved with friction stir welding, but a high ratio between the tool’s rotational and traverse speeds was required. The welding speed influenced the weld morphology and fatigue strength. The positioning of the skin materials influenced the nugget morphology and the mechanical behavior of the joints. The joints in which the AA2017 alloy was positioned on the advancing side presented the best tensile properties and fatigue strength.