Aims: A potential of rare earth elements (including yttrium) (REY) accumulation in olives is increasing due to enhanced use of REY in human activities. REY transfer to extra virgin olive oil (EVOO) is little studied, and characterising the relationships between soil properties and REY concentrations in olive leaves, pomace and EVOO can enhance our understanding of soil-plant interactions. Methods: Three different soil types (reclaimed karst, rendzina and cambisols), with the sum of REY concentrations (54–364 μg g−1) among the highest in European soils, were characterized for their pH, organic carbon, total carbonates and the applied agronomic practice. Aluminium, calcium, iron, phosphorus and REY were determined in soil (total and plant-available), olive leaves, pomace and EVOO. Results: REY were mainly excluded from plant uptake and only small amounts of REY were transferred to leaves (0.2–652 ng g−1), pomace (0.001–10 ng g−1) and EVOO (<0.5–33 pg g−1). Soil REY availability (0.001–1685 ng g−1) and plant uptake increased with increasing soil acidity. Leaf REY concentrations were mainly explained by plant-available REY and pH. There was an indication of enhanced REY plant availability being associated with low available phosphorus and soil ploughing. Conclusions: Soil properties influence REY uptake and further partitioning to leaves, fruits and EVOO.