The present research investigates the impact of eccentric shoulder tools on the microstructure and mechanical properties of friction stir welded (FSWed) aluminum alloy AA6082-T6. Two tools, one with an eccentric shoulder and one with an aligned shoulder, were employed under identical welding parameters: a rotational speed of 600 rpm, travel speed of 250 mm/min, and tilt angles of 0° and 3°. The four FSWed joints produced were characterized using optical microscopy, tensile testing, and hardness testing. The weld nugget zone (WNZ) microstructure showed significant grain size reduction from 5.24 μm for the base material to 1.63 μm, using the eccentric shoulder tool at 0° tilting angle and 2.78 μm at 3° tilting angle. The aligned shoulder tool resulted in an average grain size of 2.79 μm at 0° tilting angle and 2.23 μm of 3° tilting angle. Thus, the eccentric shoulder tool with a tilt angle of 0° exhibited the smallest average grain size. The mechanical properties obtained are consistent with the microstructure, where the joint produced using the eccentric shoulder at a 0° tilting angle showed the highest tensile strength of 216.5 MPa (89.7% joint efficiency) and 7.71% elongation. In contrast, the aligned shoulder tool resulted in coarser grains and a lower mechanical performance. In addition, this joint exhibited the highest hardness recovery in WNZ. The current study implies that the eccentric shoulder tool can eliminate the need for a tilting angle during FSW, which is required in some applications.