A major advantage of agroforestry systems is its ability to enhance soil health. Rubber and oil palm are typically cultivated in monocultures and are considered economically volatile crops. Integrating these two crops may help strengthen farmers’ resilience. This study examined a seven-year-old, innovative rubber–oil palm agroforestry system in Indonesia. Using the Biofunctool® set of indicators, the spatial heterogeneity of soil health was assessed across five distinct positions within the plot. Of the eleven indicators measured, three showed significant variation by position, which could be directly linked to specific management practices. Soil mesofauna activity was higher in less disturbed areas where cover crops were established, while nitrate dynamics was greater in zones where fertilization was applied. Infiltration rates were reduced in the rubber harvesting path, likely due to compaction from repeated walk. Most other indicators showed little variation across the plot, possibly due to the young age of the experiment and the intensive soil disturbance commonly associated with the establishment of perennial crops such as rubber and oil palm. This study provides practical recommendations for improving soil health in innovative agroforestry systems mixing rubber and oil palm. Further research incorporating agronomic and economic evaluations is needed to fully assess the system’s performance and scalability.