Apple replant disease (ARD) is a disturbance of the soil ecosystem, causing significant economic problems in fruit-growing regions and tree nurseries worldwide. The current understanding is that the soil microbial community has been affected for decades and that apple plants react with specific exudation. It is not fully understood whether these exudates, also called secondary plant products or phytoalexins, sorb in soil and contribute to the long-term persistency of ARD. We here relate the severity of ARD to soil properties such as its organic matter content, reactive mineral phases (clay), and phytoalexins. For the severity of ARD, we took plant growth parameters using the “biotest,” in which disinfected and ”unhealthy” ARD soils are compared. We analyzed Corg and the clay size fraction of soil and developed a new technique for measuring the phytoalexin content of soil, which was previously only measured in roots. Our results showed a correlation between the severity of ARD and the phytoalexin concentration in soils. The correlation between phytoalexins and Corg contents indicated that these compounds are sorbed to soil organic matter. Whether phytoalexins or their degradation products also cause ARD and play a crucial role for its persistence requires further investigation.