The Friction Stir Welding (FSW) method was employed to join AA6082 sheets. The welds were produced with different tool traverse speed (200 and 250 mm/min), rotational speed (1000 and 1250 RPM) and tool tilt angle (0 and 2 deg). Based on the analysis of XRD patterns, the total precipitation volume fractions in the nugget zones and the base material were calculated. The FSW process resulted in a reduction in the fraction of precipitates up to 64 pct compared to the parent material. Based on the Williamson–Hall analysis and indentation tests, the residual stresses were calculated. The highest tensile residual stresses of − 89.09 ± 6.19 MPa were observed for the base material, and the welding process reduced the residual stresses. The calculated dislocation density in the parent material AA6082 was equal to 8.225 × 1013 m−2, while in the welds a decrease was observed up to the value of 1.419 × 1013 m−2. In addition, the FSW process changed the nature of dislocations with edge-type dislocations dominating, while screw dominating character of dislocations were prevalent in the parent material. The mobility of dislocations in the studied welds was higher and reached the value of 16.78 × 10–7$$\frac{m}{s}$$
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, while the dislocation mobility in the parent material was equal to 3.19 × 10–7$$\frac{m}{s}$$
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. Process parameters during welding have a crucial effect on the amount of heat and strains introduced during the process, and thus influence the residual stresses, dislocation density and mobility, which might have a fundamental impact on the properties of the produced welds.