African soils host a diverse but largely underexplored fungal community, but its poorly understood nature impedes the management and understanding of vital species that provide essential ecological services. As a result, the diversity and distribution of soil fungi in Africa remain largely unknown and inadequately documented compared to the global north, with countless species and presumably higher-level taxonomic groups awaiting discovery and description. Ongoing threats such as habitat degradation, climate change, and intensified land use highlight the urgent need to understand and conserve these vital microbial communities. To address this knowledge gap, we generated eDNA metabarcoding data from 467 topsoil samples across various terrestrial ecosystems in 32 African countries. Our analyses revealed significant spatial heterogeneity, with diversity hotspots in savannas, temperate mixed forests, and dry tropical forest ecosystems and low-diversity zones (coldspots) in arid shrublands and deserts. Precipitation and latitudinal distance emerged as the strongest predictors of fungal alpha diversity. Meanwhile, the drivers of beta diversity were mainly temperature, precipitation, and soil chemical properties. To integrate African soil fungi into the principles of continental biodiversity distribution, we present a detailed continent-wide (including islands) map of fungal richness for all fungi and mycorrhizal fungi, highlighting fine-scale spatial patterns across various ecosystems. This study presents the most comprehensive spatial analysis of soil fungal diversity in Africa to date, acting as a vital reference for advancing ecological research, biodiversity monitoring, and conservation planning across the continent. We emphasize here that more effort should be made to conserve soil fungi, particularly mycorrhizal fungi in Africa, especially in regions with low fungal diversity.