In the realm of micro-Friction Stir Welding (FSW), distinct challenges arise compared to conventional FSW, encompassing faster heat dissipation through the backing surface, and higher impact of hooks on joint performance due to the reduced effective sheet thickness. Given the limited variability in tool design in micro-FSW, this study delves into the influence of pinless tool in comparison to pin tool on hook formation, temperature evolution, and bonding mechanisms. By conducting a combination of experiments and numerical investigations on 0.5 mm lap FSW joints, the study unveils that pin tool, with an 11% higher peak temperature and 46% greater effective sheet thickness, achieved 4% increase in joint strength with 26% lesser axial force during traversing. Pin tool exhibited a 10–11% higher proportion of recrystallized grains, with 11.1% and 57.6% grain refinement in the weld centre and hook regions, respectively, primarily due to pin-assisted material stirring. In contrast, pinless tool exhibited a flat nugget with directional grain growth toward the weld bottom. The pin weld demonstrated nearly three times the maximum equivalent plastic strain compared to the pinless weld, confirming the intense movement of plasticized material in the vicinity of the pin and effective intermixing across the sheet-interface.