Utilisation of wide bandgap Cd1−x Zn xS alloys as an alternative to the CdS window layer is an attractive route to enhance the performance of CdTe thin film solar cells. For successful implementation, however, it is vital to control the composition and properties of Cd1−x Zn xS through device fabrication processes involving the relatively high-temperature CdTe deposition and CdCl2 activation steps. In this study, cross-sectional scanning transmission electron microscopy and depth profiling methods were employed to investigate chemical and structural changes in CdTe/Cd1−x Zn xS/CdS superstrate device structures deposited on an ITO/boro-aluminosilicate substrate. Comparison of three devices in different states of completion—fully processed (CdCl2 activated), annealed only (without CdCl2 activation), and a control (without CdCl2 activation or anneal)—revealed cation diffusion phenomena within the window layer, their effects closely coupled to the CdCl2 treatment. As a result, the initial Cd1−x Zn xS/CdS bilayer structure was observed to unify into a single Cd1−x Zn xS layer with an increased Cd/Zn atomic ratio; these changes defining the properties and performance of the Cd1−x Zn xS/CdTe device.