The effect of electrochemical perturbation on the microstructure of transparent Sb-doped SnO2 electrode in 0.1 M NaClO4, pH 2, was investigated by in situ scanning tunneling microscopy (STM), ex situ atomic force microscopy (AFM), scanning electron microscopy (SEM), and other techniques of microstructure analysis. The transparent film of SnO2(Sb) on silica prepared by spray pyrolysis has a uniform and smooth surface with a root-mean-square (rms) roughness ranging from 1 to 2 nm. Its microstructure is constituted of coalesced particles with an average diameter and height of 30 and 6 nm, respectively. Anodic polarization at potentials near the oxygen evolution reaction region (OER) or potential cycling induces small alterations on the microstructure of the electrode, observable only in submicron range by AFM analysis. Cathodic polarization at potentials in the region of the hydrogen evolution reaction (HER), however, strongly damages the film. AFM and STM examination revealed that the particle boundaries are attacked and both vertical and lateral dimensions of the particles decrease. From the observations, it can be inferred that during the cathodic polarization SnO is formed, and destruction of the film occurs by dissolution of that more soluble oxide. In situ STM experiments showed that at the initial stages the particles of the damaged film can acquire dimensions even larger than the initial size by anodic polarization. Finally, it can be concluded that a smooth and compact film with few defects is less susceptible to degradation.