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A series of 18 ruthenium(II) polypyridyl complexes were synthesized and evaluated under electrochemically oxidative conditions, which generates the Ru(III) oxidation state and mimics the harsh conditions experienced during the kinetically limited regime that can occur in dye-sensitized solar cells (DSSCs) and dye-sensitized photo-electrosynthesis cells, to further develop fundamental insights into the factors governing molecular sensitizer surface stability in aqueous 0.1 M HClO4. Both desorption and oxidatively induced ligand substitution were observed on planar fluorine-doped tin oxide (FTO) electrodes, with a dependence on the E 1/2 Ru(III/II) redox potential dictating the comparative ratios of the processes. Complexes such as RuP4OMe (E 1/2 = 0.91 vs Ag/AgCl) displayed virtually only desorption, while complexes such as RuPbpz (E 1/2 > 1.62 V vs Ag/AgCl) displayed only chemical decomposition. Comparing isomers of 4,4′- and 5,5′-disubstituted-2,2′-bipyridine ancillary ligands, a dramatic increase in the rate of desorption of the Ru(III) complexes was observed for the 5,5′-ligands. Nanoscopic indium-doped tin oxide thin films (nanoITO) were also sensitized and analyzed with cyclic voltammetry, UV–vis absorption spectroscopy, and X-ray photoelectron spectroscopy, allowing for further distinction of desorption versus ligand-substitution processes. Desorption loss to bulk solution associated with the planar surface of FTO is essentially non-existent on nanoITO, where both desorption and ligand substitution are shut down with RuP4OMe. These results revealed that minimizing time spent in the oxidized form, incorporating electron-donating groups, maximizing hydrophobicity, and minimizing molecular bulk near the adsorbed ligand are critical to optimizing the performance of ruthenium(II) polypyridyl complexes in dye-sensitized devices.