Abstract: The bobbin tool friction stir welding process was used to join 6 mm thick 5A06 aluminum alloy plates. Optical microscope was used to characterize the microstructure. The electron backscatter diffraction (EBSD) identified the effect of non-homogeneous microstructure on the tensile properties. It was observed that the grain size in the top of the stir zone (SZ) is smaller than that in the centre region. The lowest ratio of recrystallization and density of the geometrically-necessary dislocations (GNDs) in the SZ was found in the middle near the thermo-mechanically affected zone (TMAZ) being 22% and 1.15 × 10⁻¹³ m⁻², respectively. The texture strength of the heat-affected zone (HAZ) is the largest, followed by that in the SZ, with the lowest being in the TMAZ. There were additional interfaces developed which contributed to the strengthening mechanism, and their effect on tensile strength was analysed. The tensile tests identified the weakest part in the joint at the interfaces, and the specific reduction value is about 93 MPa.