In this study, we have performed a thorough characterization of the GaN surface after etching up to 100 nm in Cl2 plasma under various bias voltages and according to the carrier wafer used (Si, SiO2, Si3N4, and photoresist). The objective of this article is to evaluate the etch damage and contamination of the GaN surface when materials with other chemical nature are present during etching. The effects of etching conditions on surface morphology and chemical compositions of etched GaN films are studied in detail using XPS and AFM measurements. To this aim, a universal methodology is proposed to estimate accurately by XPS the stoichiometry of the GaN surface exposed to reactive plasmas when only an Al Kα x-ray source is available. The results indicate that the GaN etching mechanisms are very sensitive to the chlorine radical density present in the plasma, the latter being strongly influenced by the carrier wafer. Substrates that are more chemically reactive with Cl2 plasma such as silicon or photoresist compared to SiO2 or Si3N4 will lead to a greater loading of atomic chlorine, which in turn will lead to lower GaN etch rates. Moreover, the GaN surface contamination will depend on the etch by-products ejected by the carrier wafer. The GaN surface exposed to Cl2 plasma shows a Ga-depleted surface because of the more important reactivity of Cl with Ga rather than N, except in the SiO2 carrier wafer case. In this latter case, the formation of Ga–O bond limits the Ga removal. Regarding the surface roughness, it seems that the contaminants play a little role in the roughness formation except for the oxygen released by the SiO2 carrier wafer. On the other hand, the surface roughness evolution is clearly driven by the chlorine radical flux reaching the GaN surface. At low bias voltage, a preferential crystalline orientation etching driven by the Cl radicals leads to the formation of hexagonal shaped defects that are associated to screw-type threading dislocations already present in the pristine GaN material. At higher bias, the enlargement of the defects is limited, leading to a very low surface roughness value but to amorphized surfaces.