Micro friction stir spot welding (mFSSW) is a solid-state welding method designed to join thin plates with a thickness of less than or equal to 1000 μm. This research discusses the effect of plunge depth and tool geometry on the mechanical properties and microstructure of mFSSW joints. Magnesium AZ31B with a thickness of 0.5 mm and aluminum AA1100 with a thickness of 0.42 mm were used as the base metals. The constant process parameters were a dwell time of 4 s, a plunge rate of 4 mm/min, and a tool rotational speed of 33,000 RPM. This study uses two plunge depths (400 μm and 600 μm) and four tool geometries (pinless, cylindrical, taper, and two-stage shoulder). Based on the preliminary results, the joint achieved a higher tensile load when positioning AZ31B as the upper sheet. This research’s findings indicate that plunge depth and tool geometry affect the joint strength.Higher plunge depth will result in a higher tensile load. The maximum tensile load achieved is 407.72 ± 21.19 N using a cylindrical tool at a plunge depth of 600 μm. The hardness distribution shows higher hardness in the stir zone area and gradually decreases with increasing distance from the weld center. Microstructural observations show that the metallurgical bonds formed are partially bonding and unbonding. Furthermore, observation results demonstrate the effect of tool geometry on the plate lift-up phenomenon and flash formation. © The Author(s) 2026.