A Focused Ion Beam (FIB)/lift-out technique was used to prepare site-specific thin samples of the cathode/electrolyte interface of Intermediate Temperature Solid Oxide Fuel Cells (IT-SOFC) materials. The cathode under study was a nanostructured perovskite of composition La0.4Sr0.6Co0.8Fe0.2O3-δ (LSCF) deposited by spin coating on a Ce0.9Gd0.1O2-δ (CGO) supporting substrate. We compared the results for a 15 μm and a 5 μm thickness cathode layers, before and after a thermal treatment of 1000 h at 500 °C, with the aim of simulating operation conditions. Both, Transmission (TEM) and Scanning (SEM) Electron Microscopy, coupled with Energy Dispersive Spectroscopy (EDS) systems, were used to characterize the composition and nanostructure at both sides of the cathode/electrolyte interface. To our knowledge, this is the first time that a semi-coherent interface between LSCF and CGO was observed by Electron Diffraction as well as by High Resolution TEM in many points at the interfacial boundary. A large difference in total contact area was observed between the thickest and the thinnest cathode layers, despite they present the same composition and nano sized structure. The real contact area in the 5 μm cathode sample is around 50% less than in the 15 μm sample due to the presence of pores at the interface. This observation may partially explain the difference in resistivity observed for these two half cells assemblies. On the other side, no differences were found comparing composition and nanostructure at the interface before and after the thermal treatment. Thus, this study becomes fundamental to understand the role played by the interface for improving the performance of IT-SOFC under long time operation conditions: a necessary premise for its real application.