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Transfer of trace elements, such as toxic metals, from soil to plant is a corner stone for risk assessment. Rare earth elements (REE) are frequently used as environmental tracers to understand biogeochemical processes in the soil–plant system. In this study, we combined trace element and REE measurements in the soil–plant continuum to evaluate the element transfer between different compartments. We specifically aimed at: (1) assessing the geochemical relevance and representativeness of intermediate compartments (soil solution and soil water-extract as a proxy of the bioavailable soil fraction) by comparing the REE normalized patterns; and (2) characterizing the environmental conditions that control the trace element transfer by quantifying the REE indices. For that purpose, we compared geochemical signatures in an intercropping cover crop (bean, Persian clover, and spelt) in Belgium, including soil, root, shoot, soil solution, soil water-extract, earthworm, and snow samples. Evaluation of the element mobility was performed using both soil extractability and transfer factors. The main result showed dissimilar REE patterns between soil/plant samples and soil solution/soil water-extract samples, indicating that the intermediate compartments (i.e., soil solutions or soil water-extracts) do not chemically represent the bioavailable fraction of elements without obvious propensity to biological accumulation (unlike Cd, Cu, or Zn). Compared to light REE, heavy REE were more extractable and thus transferred to plants unlike what is observed in the literature. According to their different extractabilities, Ce and Eu allowed to highlight distinct transfer from soil to plant due to possible adsorption or organic matter complexation that should be further confirmed by studying contrasted soils.