Dissimilar joints between aluminum and polymer have gained significant interest in the transportation, aerospace, and marine industries due to their potential for lightweight applications. In the present study, the joint performance analysis of dissimilar material joints of AA6061-T6 aluminum alloy and poly(methyl methacrylate) (PMMA) was performed utilizing Friction Stir Welding (FSW) in the lap joint. Shear strength testing and optical microscopy were employed to evaluate joint performance and defect formation. Joints produced using a concave shoulder tool exhibited lower thermal degradation of PMMA and improved surface quality than a flat shoulder tool. The macro- and microstructural analyses revealed joint defects such as cracks, tunnels, voids, and uneven distribution of AA6061-T6 and PMMA particles. Analysis of variance (ANOVA) revealed that rotational speed was the most influential parameter (41.16%), followed by tool geometry (34.43%) and welding speed (14.69%). The maximum shear strength of 17.8 MPa was obtained at 925 rpm and 60 mm/min using a tapered pin with a flat shoulder. Keywords: Shoulder profile, lap joint, shear strength, microstructural analysis, pore size