We present, for the first time, elemental mapping of ultra‐thin cryosections from high‐pressure frozen ectomycorrhizal roots of Picea abies–Hebeloma crustuliniforme. The maps provide interpretable information on the relationship between elements and the structure of inhomogeneous objects. Cryoultramicrotomy together with energy dispersive X‐ray microanalysis (EDX) offers the potential to study the subcellular localization of specific ions and ecologically important tracers (Cs and Sr) in ectomycorrhizal roots under conditions resembling the natural slate as closely as possible. Structural changes of the ectomycorrhizal roots, in particular the absence of a Hartig net at high NH₄⁺ levels in the nutrient solution, were accompanied by elemental modification of Ca in cortical cell walls, where markedly higher concentrations of Ca were found. Cs and Sr applied to the nutrient solution were localized in root and fungal cells of the Hartig net. Cs accumulated mainly in the vacuoles of the Hartig net hyphae and its distribution was very similar to the distribution of K. In contrast to Cs, Sr was found to occur mainly in electron‐opaque and P‐rich granules. From this study, (here is no indication that Ca is the only ion accompanying P in the P‐rich granules. Several elements including Ca, K, Cl, S, Cs and Sr, with highest concentrations for S, can occur together with P in these granules. The occurrence of the P‐rich electron‐opaque deposits in fungal cells might be the first evidence of polyphosphate granules in the native state, since our specimen preparation technique did not include chemical fixation.