Controlling the surface morphology and composition of the perovskite substrates is a critical aspect in tuning the final properties of the deposited films and of their interfaces. The paper reports on a chemical etching method developed for (110) and (001) NdGaO3 single crystal substrates in order to obtain a well-defined GaO2−x-terminated surface. The etching process is based on a HF + NH4OH solution and includes an annealing step performed in air or under O2 flow at temperatures of 800–1000 °C. In order to obtain the desired composition and surface morphology, the etching procedure was optimized for the vicinal step density at the surface and substrate crystal orientation. Growth nucleation studies of one-unit-cell MeO films (Me = Ti, Sr, Ba) on chemically etched and on only annealed substrates were performed in order to determine the composition of the substrate topmost layer. The results indicate that the chemically etched NdGaO3 substrate surface has a predominantly GaO2−x termination, with a lower free surface energy compared to the NdO1+x termination.