Trait-based approaches are useful tools to explain ecological assembly rules and ecosystem functioning. However, their use for soil microbiota has not been explored in depth yet. We explored trait-based functional changes of ectomycorrhizal (ECM) fungal communities associated with holm oak (Quercus ilex subsp. ballota) in a trace element contaminated area. We found a variation in ECM fungal species composition determined by soil C, Ca and trace elements; however, taxonomic diversity was not dependant on contamination level. Mean trait values of ECM fungal communities showed less rhizomorph and emanating hyphae production when increasing contamination, and the community converged towards species developing rhizomorphs less frequently. We suggest that trace elements in soils acted as the main environmental filter of trait diversity of ECM fungal communities. The effect of soil nutrients, i.e. soil C, affected the community mean trait values of emanating hyphae but did not cause a convergence in its distribution. In summary, we found a reduction in the functional diversity of ECM fungal communities due to trace element contamination with potential to affect ecosystem functioning. This finding supports the potential of trait-based approaches to assess changes in the functional diversity of soil microbial communities. •Metallic trace elements did not have a negative impact on ectomycorrhizal fungal taxonomic diversity.•Trace elements filtered traits in ectomycorrhizal communities.•Soil contamination was more important than soil nutrients for ectomycorrhizal community assembly.