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The microstructural evolution of Cu(In,Ga)Se₂ absorber layers during a three-stage-type co-evaporation process was studied to elucidate the effect of a Cu-rich stage on the formation of extended structural defects. Defect densities for two Cu-poor samples, one interrupted before and one after this crucial Cu-rich composition stage, were investigated by scanning transmission electron microscopy (STEM) imaging. The structure and chemical nature of individual defects were investigated by aberration-corrected high-resolution STEM in combination with electron energy-loss spectroscopy on the atomic-scale. In spite of the different defect densities between the two samples, most of the individual defects exhibited similar chemistry. In particular, the elemental distributions of atomic columns at {112} twin planes, which are very frequent in Cu(In,Ga)Se₂ thin films, were found to be the same as in the defect-free grain interiors. In contrast, within grain boundaries, dislocation cores, and other structurally more complex defects, elemental redistributions of Cu and In were observed.