Structural defects such as voids and compositional inhomogeneities may affect the performance of Cu(In,Ga)Se2 (CIGS) solar cells. We analyzed the morphology and elemental distributions in co-evaporated CIGS thin films at the different stages of the CIGS growth by energy-dispersive x-ray spectroscopy in a transmission electron microscope. Accumulation of Cu-Se phases was found at crevices and at grain boundaries after the Cu-rich intermediate stage of the CIGS deposition sequence. It was found, that voids are caused by Cu out-diffusion from crevices and GBs during the final deposition stage. The Cu inhomogeneities lead to non-uniform diffusivities of In and Ga, resulting in lateral inhomogeneities of the In and Ga distribution. Two and three-dimensional simulations were used to investigate the impact of the inhomogeneities and voids on the solar cell performance. A significant impact of voids was found, indicating that the unpassivated voids reduce the open-circuit voltage and fill factor due to the introduction of free surfaces with high recombination velocities close to the CIGS/CdS junction. We thus suggest that voids, and possibly inhomogeneities, limit the efficiency of solar cells based on three-stage co-evaporated CIGS thin films. Passivation of the voids’ internal surface may reduce their detrimental effects.