Refill Friction Stir Spot Welding (refill FSSW) shows strong potential to replace riveting in the aerospace industry. However, the complex deformation and thermal effects associated with this process lead to residual stresses that may influence the fatigue life of the joint. This study reveals for the first time the non-uniform residual stresses across the thickness of a refill FSSW aluminium joint using synchrotron X-ray radiation in combination with a conical slit cell. Clear differences can be observed in the stresses between the region subjected to plasticisation and that affected solely by heat input. A fatigue testing campaign on the aluminium joints demonstrated their high reproducibility and robustness. X-ray micro-computed tomography enabled the three-dimensional visualisation of fatigue crack nucleation and propagation morphology, the latter correlated with the tensile residual stresses in the weld area. The results can contribute to the development of more accurate fatigue life prediction models and improve the overall reliability of refill FSSW aluminium joints in engineering applications.