Most of the Dry Afromontane forests in the northern part of Ethiopia are located around church territories and, hence, are called church forests. These forests are biodiversity islands and provide key ecosystem services to local communities. A previous study of church forest fungal species was based on sporocarp collections. However, to obtain a complete picture of the fungal community, the total fungal community present in the soil needs to be analyzed. This information is important to integrate church forests into global biodiversity conservation strategies and to understand what actions are required to conserve church forests and their biological components, including fungi, which are known for their exceptionally high diversity levels. We assessed soil fungal communities in three church forests using ITS2 rDNA metabarcoding. In total, 5152 fungal operational taxonomic units representing 16 fungal phyla were identified. Saprotrophs followed by ectomycorrhizal fungi and animal pathogens dominated fungal communities. Significant differences in diversity and richness were observed between forests. Non-metric multidimensional scaling confirmed that fungal community composition differed in each forest. The composition was influenced by climatic, edaphic, vegetation, and spatial variables. Linear relationships were found between tree basal area and the abundance of total fungi and trophic groups. Forest management strategies that consider cover, tree density, enrichment plantations of indigenous host tree species, and environmental factors would offer suitable habitats for fungal diversity, production, and function in these forest systems. The application of the baseline information obtained in this study could assist other countries with similar forest conservation issues due to deforestation and forest fragmentation.