Energy dispersive X-ray fluorescence (EDXRF) spectroscopy is an analytical technique often used to create maps of the elemental chemical composition. The fluorescence signal can be influenced by X-ray diffraction peaks, a phenomenon that can lead to difficulties or errors in interpreting spectral peaks. However, diffraction can also be useful if we successfully separate it from the fluorescence signal. In this paper, we propose different methods to deal with the diffraction peaks by using the signals obtained from a spectrometer equipped with two detectors. These methods were tested on a thin section of a rock sample to show their effectiveness in processing diffraction peaks. Each method showed its ability to deal with the diffraction peaks in a more or less effective way and each has its own limitations. The latter have to be taken into account when analyzing the EDXRF signal, whether in a geological context or in any other context.