The spontaneous formation of double chemical terminated surfaces of La0.7Sr0.3MnO3 due to deviations from ideal epitaxial growth during its deposition on SrTiO3(001) is presented. The development of surface regions with differentiated topmost composition leads to outstanding surface nanostructuration presenting notably distinct local properties, particularly in terms of electric transport and local work function. Correlation between combined atomic force microscopy and X-ray photoelectron spectroscopy data allows the chemical identification of the two terminations as corresponding to La0.7Sr0.3O and MnO2. The most likely atomistic process at the origin of the surface organization has been interpreted by Monte Carlo simulations that reveal the importance of stacking fault formation as growth proceeds. We present a physical understanding of the experimental results for surfaces in which different electronic responses coexist. The conclusions of the present work can be extended to the growth of other perovskite thin films, therefore broadening the field of functional materials nanostructuration.