In most studies conducted on friction stir spot welding, the focus has been on process parameters and the tool pin geometry. One of the influential parameters in this process, which has received less attention, is the tool shoulder diameter. The spread or concentration of the weld can significantly affect the weld strength and mechanical properties of the joint. In this research, two tools made of H13 hot-work steel with different shoulder diameters of 20 and 25 mm were prepared. Three rotation speeds of 1000, 1600, and 2400 rpm were considered for the welding process. The arrangement of aluminum plates on top of each other was varied in two configurations, parallel and overlapped. Mechanical properties, including tensile shear strength and Vickers micro-hardness, were investigated. The microstructure of different weld zones was also examined using an optical microscope. The results showed that increasing the tool shoulder diameter could enhance the breaking force and tensile shear strength of the joints. Meanwhile, the rotation speed had an optimal value, and with its increase, the breaking force initially increased and then decreased. Placing the 2024-T3 aluminum plate on top of the stack also increased the tensile shear strength of the samples. The fracture mode of the broken specimens was entirely nugget pull-out, which became more pronounced during the use of optimal parameters. Micro-hardness in the region influenced by heat decreased, reaching a minimum in the thermo-mechanically affected zone. In the stir zone, micro-hardness increased significantly due to intense plastic deformation and material compression. The microstructure in the nugget region appeared fine-grained and compact, while the region affected by coarse grain experienced significant heat effects. Increasing the tool shoulder diameter led to an increase in the nugget zone and the length of the bonded region. However, it did not have a significant effect on grain size in the nugget region.