Fluorine plays an important role in magmatic and hydrothermal processes, but due to its low abundance in geological samples determining F is difficult by electron probe microanalysis. By using a W‐Si multi‐layered pseudocrystal as the diffraction crystal instead of thallium acid phthalate (TAP), count rates were considerably higher, which however introduced spectral interferences between FKα and FeLα and MgKβ lines when normal integral mode is applied. In this study, we developed a protocol using a W‐Si multi‐layered pseudocrystal for measuring accurately trace level F in both minerals and glasses. First, we used differential mode with an optimised PHA (pulse height analysis) setting in signal processing, instead of normal integral mode, which completely eliminated the second‐order MgKβ line. Second, the overlap of the first‐order FeLα on FKα peak, which cannot be filtered by modifying the PHA setting, was calibrated quantitatively using F‐free minerals and silicate glasses. Applying this two‐step method, F was determined in a number of reference glasses, as well as in glasses synthesised from powders of the rock reference materials AC‐E, GS‐N and DR‐N. Our data are consistent within error with F concentrations determined by other methods, demonstrating the reliability of this method.