Residual stresses play a significant role in determining structural component properties, including strength, fatigue performance, and corrosion behaviour. Refill Friction Stir Spot Welding (refill FSSW) exhibits great potential to substitute single-point joining methods such as riveting, which can directly impact the automotive and aeronautics industry. However, the complex interplay of nonuniform plastic deformation, thermal gradients, heterogeneous material flow, and rapid microstructural changes during refill FSSW inevitably leads to residual stresses. This study provides a comprehensive three-dimensional analysis of the residual stress field in refill FSSW joints using synchrotron X-ray radiation in combination with conical slits, revealing a non-uniform stress distribution across the thickness of the welded sample. Unlike prior studies that assumed plane stress conditions due to the relatively small sheet thickness, our findings indicate remarkable compressive stresses in the normal direction and significant variations between areas affected by plasticity and those influenced by heat input alone.