Different challenges associated with dissimilar micro-friction stir welding result in improper material inter-mixing, which affects joint integrity. The present work used a triple-spiral micro-grooves featured tool to miti-gate this issue while joining 0.5 mm thick AA6061-T6 and ALCLAD 2024-T3 alloy sheets. The extent of material intermixing and its flow due to the introduction of micro-grooves on the shoulder-end surface was assessed by analyzing process responses, and weld characteristics. This investigation was further extended for different micro-groove depths (0.06 mm, 0.09 mm, and 0.12 mm). Apart from the types of material flow (continuous and discontinuous) through the micro-grooves, the difference in the interaction volume with the shoulder-end surface also affected the process responses and the weld characteristics. The defect-free welds obtained in different cases were considered for detailed microstructural analysis at the center of the stir zone and the junction of the two materials to correlate with the weld performance. It was found that finer grains (1.954 +/- 0.973 mu m), a high percentage of recrystallized grains (84.5%), and high angle grain boundaries (61.5%), with high texture intensity (3.301) were obtained in the stir zone of the weld produced by the highest micro-groove depth (0.12 mm) tool. This was attributed to the high degree of material intermixing at the highest micro-groove depth since it facil-itated a higher volume of material to be directed both in the thickness direction and from one side of the weld to another. As a result, improved tensile properties with the highest mean joint efficiency of 77.18% were obtained where the weld fractured from the heat-affected zone of the AA6061 side.