Elemental intermixing at the CdS/CuIn1−xGaxSe2 (CIGS) heterojunction in thin‐film photovoltaic devices plays a crucial role in carrier separation and thus device efficiency. Using scanning transmission electron microcopy in combination with energy dispersive X‐ray mapping, we find that by controlling the oxygen in the sputtering gas during physical vapor deposition (PVD) of the CdS, we can tailor the degree of elemental intermixing. More oxygen suppresses Cu migration from the CIGS into the CdS, while facilitating Zn doping in the CdS from the ZnO transparent contact. Very high oxygen levels induce nanocrystallinity in the CdS, while moderate or no oxygen content can promote complete CdS epitaxy on the CIGS grains. Regions of cubic Cu2S phase were observed in the Cu‐rich CdCuS when no oxygen is included in the CdS deposition process. In the process‐of‐record sample (moderate O2) that exhibits the highest solar conversion efficiency, we observe a ~26‐nm‐thick Cu‐deficient CIGS surface counter‐doped with the highest Cd concentration among all of the samples. Cd movement into the CIGS was found to be less than 10 nm deep for samples with either high or zero O2. The results are consistent with the expectation that Cd doping of the CIGS surface and lack of Zn diffusion into the buffer both enhance device performance.