T-joints are common structures encountered in the assemblage of many industrial applications due to their advantages. However, joining these structures when using Friction Stir Welding (FSW) could be prone to defects that cause severe consequences like loss of strength and fracture. The current paper implements an experimental procedure to assess the effect of geometrical tool shape on void formation in friction stir welded AA 6061-T6 T-joint configuration. Taguchi optimization method was put into service to minimize the number of experiments and fulfil the goal of discovering the optimal FSW parameters that allow the manufacturing of such configurations with high mechanical properties. X-ray radiography and micrograph images were used to capture the defect type in AA 6061 T-joints using nine different profiles. Four different dimensional variables (pin diameter (mm), shoulder diameter (mm), pin angle (α, deg), and groove pin shape) with three levels for each variable have been practiced. Thermal environment and microhardness properties were also recorded to investigate macrostructure and joint strength. The accompanying thermal environment for the nine different cases was recorded using thermocouples and infrared measurements. The results showed that tools having specifications of (shoulder diameter = 17.1 mm, pin diameter = 2.2 mm, pin angle = 5°, and pin groove shape = right-handed), or (shoulder diameter = 17.1 mm, pin diameter = 2.7 mm, pin angle = 10°, and pin groove shape = left-handed) can return free of defects T-joint samples. The maximum temperature recorded during the FSW process was less than the melting point of the AA6061 alloy, which ensures the suitability of FSW to joining heat-sensitive alloys.