The development of the microstructure and mechanical properties during friction stir welding of 6063-T4 aluminium alloy was investigated through electron backscatter diffraction (EBSD) and transmission electron microscopy (TEM) techniques and mechanical testing. Grain boundary and dislocation strengthening were observed to be the dominant strengthening mechanisms occurring in the stir zone (SZ). While the precipitates morphologies were sensitive to the weld zone temperatures, the grain size and grain boundary misorientations were related to strain (ϵ), strain rates (ϵ̇), and peak temperatures (Tp). Severe gradients in the crystallographic texture were observed at the top and bottom and on the retreating and advancing sides of the weld obtained at 48 mm/min welding speed. The optimal strength and ductility of a transverse tensile specimen were achieved when the cold defects, overaging in heat affected zones (HAZs), and grain size in stir zone (SZ) were minimized. While the yield strength of the longitudinal tensile specimens was controlled by the grain size, dislocation density and fraction of low angle boundaries (LABs), the uniform elongation was controlled by the fraction of high angle boundaries (HABs). In addition, a successful implementation of more simple geometry weld zone finite element model than earlier reported work for use in forming simulations was also proposed. © 2016, Springer-Verlag London.