In polycrystalline thin-film cadmium telluride (CdTe) solar cells, atomic defects (dopants: copper (Cu), arsenic (As); and selenium (Se) alloy) have significantly enhanced hole density and minority carrier lifetime. Density functional theory (DFT) has predicted the atomic configurations of relevant defects and their electronic structures. Yet, experimental evidence of the defects, especially their spatial distribution across the absorber, is still lacking. Herein, since it can probe local atomic structure of elements of interest with trace-elemental sensitivity, nanoprobe X-ray absorption near edge structure (XANES) spectroscopy was used to elucidate atomic structures of Cu, As, and Se. After XANES spectra were measured from CdTe devices, the atomic information was extracted from the measured spectra by fitting them with reference spectra, which were simulated from 1) point defects and grain boundaries (GBs) predicted by DFT; 2) secondary phases which could form under processing conditions. XANES analysis of various device architectures revealed structural inhomogeneities across the absorbers from point defects to secondary phases. The majority of the Cu dopant atoms form secondary phases with surrounding atoms even inside the absorbers, explaining the low dopant activation. When entering the target lattice site (Cd), Cu forms a complex with chlorine (Cl) and becomes a donor defect, compensating hole density. Compared to Cu, As dopant tends to enter the target site (Te) more frequently, explaining higher hole density in As-doped CdTe. Notably, As on the Te site forms neutral charged complexes with Cl. Although they are not as detrimental as the Cu-Cl complex, the As-Cl complexes may be responsible for low dopant activation and compensation observed in As-doped CdTe devices. Complementary to the DFT prediction, this work provided the distribution of Se local structures across the absorber, specifically the variation of Se-Cd bond lengths in differently performing areas. Under environmental stressors (heat and light), it showed atomic reconfiguration of Se and Cl at GBs, and Se diffusion into the bulk, co-occurring with device degradation. This framework was also extended to study defect evolution in other thin-film solar cells (CIGS and emerging perovskite). XANES analysis has shed light on atomic defects governing solar cell performance and stability, which are crucial in pushing the efficiency toward the theoretical efficiency limit.