Although Friction Stir Welding (FSW) is broadly invested in joining aluminum alloys, welding T-joint configurations display revealing challenges due to the interface’s intricate material flow and stress development. Defect formation, including voids and lack of fusion, as well as sudden response forces and residual stresses, can substantially undermine joint performance. This study presents an innovative three-dimensional finite element model to predict the coupled thermomechanical conditions experienced during the friction stir welding (FSW) of AA 6061-T6 lap T-joint design. The study identifies the geometrical parameters of the FSW tool, including shoulder and pin diameters, as well as pin form (cylindrical and tapered), as critical variables affecting thermal and mechanical outcomes. Three distinct tool geometries (T1, T2, T3) were evaluated to achieve the objectives of the current mission of FSW of the AA6061 lap T-joint. This work employs the Coupled Eulerian–Lagrangian (CEL) finite element modality to anticipate and analyze factors influencing the service life of the friction stir welded T-joint. Temperature, plastic strain, von Mises stress, defect type, and force feedback on the tool generated over the fabrication of the T-joint structure were recorded and studied. Alongside thermocouples, infrared cameras were employed to assess the temperature history to validate numerical results, and macrostructural micrographs were produced to identify the type of voids. The findings indicated that the CEL finite element model overestimates the temperature by a maximum of 7% for the T3 tool shape. The plastic strain was more pronounced on the advancing side than on the retreating side. The von Mises stress exhibited an M-shaped distribution, reaching a maximum value of 70 MPa for the T2 tool. The CEL model demonstrated notable ability in capturing the sort of void produced by three distinct tools.