Aims <p>Soil protists are phylogenetically and functionally diverse microscopic eukaryotes that play key roles in nutrient cycling, microbial filtering, and soil food-web stability. However, the drivers shaping their diversity and community composition remain poorly understood.</p> Methodology <p>Using a 50-year-old common-garden experiment in Denmark with six European tree species representing arbuscular mycorrhizal (AM)(e.g. ash and maple) and ectomycorrhizal (ECM)(e.g. lime, beech, oak, and Norway spruce) associations, we combined high-throughput 18S rRNA gene amplicon sequencing of DNA with detailed analyses of soil physicochemical properties and litter quality to assess how tree species, mycorrhizal association, and land-use legacy shape soil protist communities.</p> Results <p>Protist alpha diversity varied significantly among tree species, driven mainly by litter quality rather than soil properties. AM-associated ash supported higher richness than ECM-associated spruce and former forest soils hosted greater diversity than former croplands. Beta diversity was influenced by tree species and soil chemistry; AM species were linked to higher pH and low C:N ratios, whereas ECM species were associated with greater organic carbon and higher C:N ratio. Apicomplexa dominated across all soils, likely reflecting their high dispersal potential and ecological resilience in terrestrial environments. Different protist groups responded to litter and soil properties: Stramenopiles thrived in alkaline, nutrient-rich soils; Cercozoa and Ciliophora in nutrient-poor, high C:N soils; whereas Amoebozoa showed no clear correlations.</p> Conclusions <p>This long-term experiment demonstrated that tree species identity and traits; mediated through litter quality, soil management, and soil properties; are key determinants of soil protist diversity and community structure.</p> Graphical Abstract <p></p>