In solid-state welding, the basis of joining is the combination of materials in the weld area using the tool. The tool pin is a key parameter that can facilitate tool penetration into the parts and result in better material mixing. On the other hand, the presence of the end cavity of the process can be a factor in reducing the mechanical properties of the weld. To address these two conflicting issues, this study examined the effect of pin thickness on the mechanical and metallurgical properties of aluminum 6061 and 5052 plates. The variable parameters included pin diameters (4 mm, 8 mm, and no pin) and three tool penetration depths (0.5 mm, 1.5 mm, and 2.5 mm). The impact of changing the arrangement of the plates on each other was also investigated regarding the properties and quality. Experimental results showed that decreasing the pin diameter and increasing the tool penetration depth improved the weld breakage force. The failure modes of all welds were button pull-out and ductile failure. Using a pinless tool increased microhardness in the weld nugget area and led to more uniform microhardness variations. Placing the aluminum 6061 alloy on top of the arrangement improved shear tensile strength and microhardness of the joints. The microstructure in the heat-affected zone showed an increase in grain size, which was accompanied by a decrease in microhardness. The microstructure in the stirred zone was dense and compacted, and with increasing tool penetration depth and decreasing pin diameter, the grain size became finer.