The European Union aims to achieve healthy soils by 2050. To support this goal, a soil monitoring system that facilitates both local soil management and political decision-making must be considered across space and time. Here, we introduce a Pan-EU soil monitoring system that combines local soil observations with updated maps of soil health indicators. First, we developed Soil Monitoring Units (SMUs) based on similar pedoclimatic conditions (climate and soil types) across the EU. These SMUs provide the spatial framework for comparing and analysing soil health indicators, enabling farmers to assess their soil conditions relative to peers who share the same natural conditions. This step is crucial for generating local information, thresholds, and targets for soil health evaluation and future management. Second, we integrated the threshold values for each soil health indicator within SMU into existing soil health indicator maps, spatially highlighting areas that fall outside the typical value ranges. This approach can inform policy decisions at the EU, national, and regional levels by identifying areas where soil health indicators deviate from the norm and where corrective measures should be taken. These initial steps aim to establish a baseline and provide valuable insights for setting thresholds and targets, which can be compared with future soil monitoring campaigns. This is especially important in the absence of reference values, as relative changes can indicate the direction of soil health development. Furthermore, identifying areas with more significant problems can guide EU soil sampling efforts to prioritize regions experiencing high soil degradation or risk. The feedback loop in this monitoring system across space and time with identification of risk zones, target soil sampling and measures to improve soil conditions will help achieve the goal of healthy soils by 2050.