Eucalyptus tree species are widely used in Ethiopian plantations, but the impact of these plantations on the soil fungal communities is still unknown. We assessed the changes in diversity, species composition and ecological guilds of the soil fungal communities across tree ages of Eucalyptus grandis plantations by DNA metabarcoding of ITS2 amplicons. Changes in soil fungal species composition, diversity and ecological guilds were related to stand age but also to fertility changes. The relative abundance of saprotrophs and pathogens were negatively correlated with stand age, and positively with soil fertility. In contrast, the relative abundance and diversity of ectomycorrhizal species were higher in older, less fertile stands, including well-known cosmopolitan species but also species associated with Eucalyptus, such as Scleroderma albidum and Descomyces albellus. We show that soil fungal community changes are linked to progressive soil colonization by tree roots but are also related to soil fertility changes.