The AA6082-T6 and AA5754-H22 aluminium alloys were selected as the base materials to fabricate similar and dissimilar friction stir lap welds. Three lap configurations, AA6082/AA5754, AA5754/AA6082 and AA6082/AA6082, were produced using three pin profiles and tested to analyse the role of the plastic behaviours of the base materials on the welding conditions. The macrostructural characterisation was carried out to understand the material flow response and hook defect formation. The mechanical characterisation of the joints was done by microhardness and lap tensile shear testing. The finite element analysis and phase simulation were conducted to predict the phase dissolution temperatures and the softening kinetics. The welding torque and axial forces registered were analysed to quantify differences in the alloy’s flowability during welding. The analysis of the welding machine outputs enabled to conclude that higher axial forces were registered when the AA5754 alloy was placed at the top of the dissimilar lap joint, showing that the non-heat-treatable alloy has lower flowability than the heat-treatable alloy. These results were associated with the flow-softening of the AA6082 alloy in plastic deformation at high temperatures. The coupled experimental and numerical analysis revealed that the plastic behaviour of the base materials strongly influenced the material flow and, in this way, the hook defect formation and the shear tensile properties of the welds.