Characterisation of cement clinkers is a prerequisite to optimise properties of cements and concretes. Therefore, the protocol to prepare and characterise cement clinkers using electron backscatter diffraction (EBSD) in combination with energy dispersive X-ray spectrometry (EDS) is described. It is shown that argon broad ion beam polishing delivers surfaces with high contrast electron backscatter diffraction patterns (EBSP). EBSD data quality in high and low vacuum SEM reveals that high vacuum conditions and state-of-the-art EBSD cameras deliver EBSPs of cement clinker at improved quality. Furthermore, exemplary EBSD-EDS analysis is discussed for two Portland cement clinkers. Results clearly show that differentiation between major phases can reliably be achieved. In addition, it is revealed that crystal distortion in belite is high. Analysis of C3A phases show that differentiation of orthorhombic and cubic polymorph is possible, and that Mg incorporation leads to amorphization. Results demonstrate that EBSD-EDS analysis allows reliable phase characterisation of cement clinkers.