In order to meet the escalating demand in the shipbuilding business, suitable materials with enhanced qualities are required to maximize ship cargo while reducing fuel consumption. Aluminum (Al) and its alloys are competing contenders for use in a variety of complicated ship structures. The major challenge to enhancing joint quality and performance is the quest for a viable and efficient FSW parameter. The main focus of this study was to critically explore the effect of the tool pin profile and the preheat temperature used during the friction stir welding of AA 5052-H32 on its mechanical properties and weld microstructure characteristics. There are three pin profile variations, including samples that were cylindrical, samples with two flat sides, and samples with three flat sides, all of which were investigated in different preheat temperatures (150–300 °C). The results that were obtained during macrographic observation showed that tunnel defects were visible in the cylindrical and two-flat-sided pin profile designs. During observations of the microstructure, it was observed that the grain size became finer and smaller in the weld nugget compared to in the heat affected zone (HAZ) and thermo-mechanically affected zone (TMAZ) regions due to dynamic recrystallization. However, at the 300 °C preheat variation, the grain size appeared to be larger due to the slower cooling rate, causing a decrease in the mechanical properties of the samples. The results of the physical tests determined that the preheat temperature caused an increase in the mechanical properties until 250 °C, at which point the three-flat-sided pin profile tool demonstrated superior mechanical properties compared to the tools with a cylindrical design; a 12.2% tensile strength increase, a 15.3% and 9.4% face and root bending increase, and an 11.2% hardness increase were observed.