The microstructural, tribological, and mechanical performance of friction-stir welded AA6061-T6 and AZ31 alloys were investigated using electron back scattered diffraction, scanning electron microscope, X-ray diffraction, and electron dispersed spectroscopy methods. The non-destructive X-ray microcomputed tomography test was used to analyse weld porosity. The distribution of volumetric and surface flaws (pores) was found to be confined across the weldment. Using a novel atomic force microscopy method, the nano-tribological characteristics of the base metal and localized regions of welded sample were studied for the first time. The significant difference in wear and friction behaviour was observed in all weld zones and base metal of magnesium side, which was correlated with the hardness of these regions. AFM results showed strong variation in tribological properties in correlation with the hardness trends of different weld zones, i.e. higher hardness leads to low wear. In weldments, intermetallic compounds such as Al12Mg17 and Al3Mg2 were produced, resulting in nanohardness differences as measured by the nanoindentation test. The joint efficiency of 65%, 84%, and 91% were obtained at welding speeds of 16 mm/min, 20 mm/min, and 25 mm/min, respectively.