In our work, Al-Mg-Si (6061Al -T4) plates of 6 mm thickness were subjected to bobbin tool friction stir welding (BT-FSW) and conventional friction stir welding (C-FSW) for comparison. How the welding process affects the microstructure and mechanical properties was investigated at various rotation rates and welding speeds. The results showed that butt FSW joints with high quality could be produced at the selected parameters. The joint strength rose with enhanced welding speed and was nearly independent of the rotation rate in both the welding processes. The strength of the joints produced with BT-FSW reached the same level as that of the C-FSW. The maximum joint strength of 229 MPa was 93% of the base material (BM), which is superior to the reported results of 60–80% for the T4 condition. The fracture position of most of the joints was in the heat-affected zone (HAZ), which is the lowest hardness zone.