Poly(vinylpyrrolidone) (PVP)-stabilized Pd nanocubes were synthesized, deposited on a carbon-based support, and subsequently treated with UV–ozone (UVO) in order to eliminate the traces of PVP still present on the surface. Cubes, being a thermodynamically unfavorable shape, are very prone to restructuring to minimize the interfacial free energy and thus allow the assessment of their morphological stability during UVO cleaning. The process of PVP removal was monitored by X-ray photoelectron spectroscopy (XPS), X-ray diffraction (XRD) and in situ attenuated total reflection infrared spectroscopy (ATR-IR). High-resolution scanning electron microscopy (SEM) imaging was used to evaluate the morphology of the nanocubes. The effect of PVP removal was also studied in the hydrogenation of acetylene, showing a 4-fold increase of activity. This method can be applied to nanoparticles of other common shapes, which expose different crystal planes, in order to study the structure sensitivity of chemical reactions.