Synchrotron‐based X‐ray tomographic microscopy is investigated for imaging the local distribution and concentration of phosphoric acid in high‐temperature polymer electrolyte fuel cells. Phosphoric acid fills the pores of the macro‐ and microporous fuel cell components. Its concentration in the fuel cell varies over a wide range (40–100 wt% H3PO4). This renders the quantification and concentration determination challenging. The problem is solved by using propagation‐based phase contrast imaging and a referencing method. Fuel cell components with known acid concentrations were used to correlate greyscale values and acid concentrations. Thus calibration curves were established for the gas diffusion layer, catalyst layer and membrane in a non‐operating fuel cell. The non‐destructive imaging methodology was verified by comparing image‐based values for acid content and concentration in the gas diffusion layer with those from chemical analysis.