The interest in agroforestry systems has increased considerably in recent years. The systems are more resilient to climate change and offer advantages related to soil health and biodiversity. Although the aboveground impacts of agroforestry systems are well known, the knowledge concerning root growth of trees remains limited. This study tested the applicability of a non-destructive investigation method, the ground penetrating radar (GPR), to detect tree roots. We mapped two 80-year-old pear trees in cropland and investigated the impact of tilled and no-tilled management on the root system architecture especially in deeper soils (>0.6 m). The root mapping method was successful, we determined the main roots of the tree up to a depth of 0.75 m. In addition, we found tillage significantly impacted root distribution. Tillage removed tree roots almost completely to a depth of 0.4 m. The bulk of the roots was present at a depth of 0.6 to 0.75 m (83% of the roots) in the tilled section, while it was found at 0.3 to 0.55 m (74%) in the no-tilled section. Detected roots indicated an overcompensation by additional roots in the tilled section that were not formed without tillage. Overall, we found agroforestry trees were rooting deeper, below the managed cropland and therefore colonise different soil layers. Thus, the potential volume of water and nutrient intake was enlarged, which might enhance the resilience of the combined production systems. In addition, our approach presents a method for future non-destructive and continuous monitoring of tree roots and their development. •Testing GPR system to detect deep root interaction in agroforestry systems.•Arable crops and agroforestry tree roots colonise different soil depths.•Tillage impacted tree roots by removal in topsoil and overcompensation in subsoils.•Non-destructive monitoring method of tree root system and their development.