Electron backscatter diffraction (EBSD) is a powerful technique for surface microstructure analysis. EBSD analysis of cubic yttria-stabilized zirconia (YSZ) is demonstrated. The statistics related to EBSD indexing reliability shows that the probability of accurate grain orientation detection increased significantly when the electron beam energy was increased from 10 to 30 kV. As a result of better sampling with increased interaction volume, a disparity between local and average grain misorientation angle also exhibited the dependence of the electron beam energy to determine the accuracy of grain orientation. To study EBSD indexing reliability as a function of surface roughness and overlayer formation, rapid EBSD measurement tests were performed on (a) YSZ surfaces ion-polished at ion beam energies of 65 nA at 30 kV and 1 nA at 30 kV and (b) carbon-coated versus uncoated YSZ surfaces. The EBSD results at both 10 and 30 kV electron beam energies indicate that EBSD indexing reliability is negatively affected by higher ion beam milling current and amorphous overlayer formation.