The present work aims at investigating the microstructure of Zn(O,S) buffer layers relative to their deposition route, namely either chemical bath deposition (CBD) or RF co-sputtering process (PVD) under pure Ar. The core of the study consists of cross-sectional transmission electron microscopy (TEM) characterization of the differently grown Zn(O,S) thin films on co-evaporated Cu(In,Ga)Se2 (CIGSe) absorbers. It shows that the morphology of Zn(O,S) layer deposited on CIGSe using CBD process is made of a thin layer of well oriented ZnS sphalerite-(111) and/or ZnS wurtzite-(0002) planes parallel to CIGSe chalcopyrite-(112) planes at the interface with CIGSe followed by misoriented nanometer-sized ZnS crystallites in an amorphous phase. As far as (PVD)Zn(O,S) is concerned, the TEM analyses reveal two different microstructures depending on the S-content in the films: for [S] / ([O] + [S]) = 0.6, the buffer layer is made of ZnO zincite and ZnS wurtzite crystallites grown nearly coherently to each other, with (0002) planes nearly parallel with CIGSe-(112) planes, while for [S] / ([O] + [S]) = 0.3, it is made of ZnO zincite type crystals with O atoms substituted by S atoms, with (0002) planes perfectly aligned with CIGSe-(112) planes. Such microstructural differences can explain why photovoltaic performances are dependent on the Zn(O,S) buffer layer deposition route.