Autotoxic compounds are likely to be among the causes of apple replant disease, but their secretion is low during plant life. Using targeted metabolomics, the changes in soil phenolic profile were analyzed after the addition of apple roots, and their potential autotoxicity was assessed on apple seedlings. The addition of apple roots severely damaged the plants, attributed to autotoxic action of the phenolic compound phlorizin. Prolonged residence time of the roots in the soil before planting reduced their negative action, probably due to the degradation of phlorizin.