SUMMARY: At the morphological and anatomical levels, the ionome, or the elemental composition of an organism, is an understudied area of plant biology. In particular, the ionomic responses of plant–pathogen interactions are scarcely described, and there are no studies on immune reactions. In this study we explored two X‐ray fluorescence (XRF)‐based ionome visualisation methods (benchtop‐ and synchrotron‐based micro‐XRF [µXRF]), as well as the quantitative inductively coupled plasma optical emission spectroscopy (ICP‐OES) method, to investigate the changes that occur in the ionome of compatible and incompatible plant–pathogen interactions. We utilised the agronomically important and comprehensively studied interaction between potato (Solanum tuberosum) and the late blight oomycete pathogen Phytophthora infestans as an example. We used one late blight‐susceptible potato cultivar and two resistant transgenic plant lines (only differing from the susceptible cultivar in one or three resistance genes) both in control and P.infestans‐inoculated conditions. In the lesions from the compatible interaction, we observed rearrangements of several elements, including a decrease of the mobile macronutrient potassium (K) and an increase in iron (Fe) and manganese (Mn), compared with the tissue outside the lesion. Interestingly, we observed distinctly different distribution patterns of accumulation at the site of inoculation in the resistant lines for calcium (Ca), magnesium (Mg), Mn and silicon (Si) compared to the susceptible cultivar. The results reveal different ionomes in diseased plants compared to resistant plants. Our results demonstrate a technical advance and pave the way for deeper studies of the plant–pathogen ionome in the future. Significance Statement: Using benchtop and synchrotron µXRF imaging and ICP‐OES quantification, we analysed the ionomic changes in potato (Solanum tuberosum) plants upon inoculation with the late blight pathogen Phytophthora infestans. Inoculation with the pathogen leads to shifts in the distribution patterns of several elements in either susceptible or resistant potato leaflets, including a particular redistribution of manganese (Mn) and silicon (Si) in R‐gene‐containing lines. These techniques open up new possibilities for plant–microbe interactions research at the ionome level. [ABSTRACT FROM AUTHOR]