Recent magnetotransport and neutron scattering measurements implicate interfacial magneto-electronic phase separation as the origin of the degradation in transport and magnetism in ultra-thin film La1-xSrxCoO3on SrTiO3(001). Here, using low temperature scanning tunneling microscopy and spectroscopy the first direct, real space observation of this nanoscopic electronic inhomogeneity is provided. Films of thickness 12.4-nm (32 unit cells) are found to exhibit spatially uniform conductance, in stark contrast to 4.7-nm (12 unit cell) films that display rich variations in conductance, and thus local density of states. The electronic heterogeneity occurs across a hierarchy of length scales (5-50-nm), with complex correlations with both topography and applied magnetic fields. These results thus provide a direct observation of magneto-electronic inhomogeneity in SrTiO3(001)/La0.5Sr0.5CoO3at thicknesses below 6-7-nm, in good agreement with less direct techniques.