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Studies based on metal isotope changes at micro-scale interfaces within soils (i.e., between aggregates of different size fractions) can provide further insight into soil-plant interactions during long-term phytoextraction. Here, aggregate size separation was conducted on two contaminated soils that underwent phytoextraction using Zn/Cd hyperaccumulator Sedum plumbizincicola over six consecutive seasons. The dynamic changes in Zn and Cd concentrations, chemical fractionations and isotope compositions in soil aggregates were investigated. As phytoextraction proceeded from the first (C1) to the sixth (C6) season, shoot Zn displayed a marginally heavier isotope composition despite the essentially constant Zn isotope composition of bulk soils and the 50–250, 5–50, 1–5, and