The surface structures of SrTiO 3 (100) single crystals were examined as a function of annealing time and temperature in either oxygen atmosphere or ultra-high vacuum (UHV) using noncontact atomic force microscopy (NC-AFM), Auger electron spectroscopy (AES), and low-energy electron diffraction (LEED). Samples were subsequently analyzed for the effect the modulation of their charge distribution had on their surface potential. It was found that the evolution of the SrTiO 3 surface roughness, stoichiometry, and reconstruction depends on the preparation scheme. Surface roughness evolved non-monotonically with UHV annealing temperature, which is explained by electrostatic modulations of the surface potential caused by increasing oxygen depletion. This was further corroborated by experiments in which the apparent roughness tracked in NC-AFM could be correlated with changes in the surface charge distribution that were controlled by applying a bias voltage to the sample. Based on these findings, it is suggested that careful selection of preparation procedures combined with application of an electric field may be used to tune the properties of thin films grown on SrTiO 3 .