Plant and soil diversity are closely connected, yet how environmental factors drive their coexistence across Africa at fine spatial scales is poorly understood. This gap stems in part from studying each component in isolation. Using 17,000 observations at 250 m resolution and combining machine learning with interpretable statistical models, we examined the pan-African links between plant and soil diversity. We found that drivers such as slope, mean annual temperature, and groundwater depth shape this relationship in distinct ways, leading to a highly varied spatial pattern across the continent. The equal strength of reciprocal effects between plants and soils points to a tightly connected system where environmental factors act together. Our results highlight the fine-scale interactions between plant and soil diversity, offering insights for targeted monitoring and supporting joint conservation of African plants and soils across environments from deserts to tropical forests.