In-situ functionalization of polar GaN was performed by adding cysteamine to a phosphoric acid etchant in order to study its effect on photoluminescence and oxide formation on the surfaces. The functionalization was characterized by atomic force microscopy, x-ray photoelectron spectroscopy, photoluminescence (PL), and water contact angle measurements. Two sets of polar GaN samples with different dislocation densities were evaluated, thin GaN layers residing on sapphire and thick free-standing GaN separated from sapphire substrate aiming to reveal the effect of material quality on in-situ functionalization. The addition of cysteamine to the phosphoric acid solution was found to result in: (i) decreased surface roughness, (ii) no change to hydrophobicity, (iii) decreased oxygen content especially at high-temperature treatments. The effect of the in-situ functionalization on the PL efficiency was more pronounced in the free-standing sample than in the film residing on the sapphire, which was attributed to a higher crystal quality free from strain.