Urbanisation, as a global driver of change, modifies the natural environment with well-known consequences to biological communities. Under natural conditions, vegetation drives soil processes in concert with the soil microbial community in their rhizosphere. It remains unclear whether and how vegetation influences these communities in heavily disturbed urban systems where many ecosystem services are also strictly linked to soils and their biota. Here, we used amplicon sequencing and GeoChip arrays to study soil microbiota responses to urbanisation and tree functional types across climatic zones. Our data show that soil microbial communities vary widely across biomes, yet urban parks have compositionally unique microbial communities that are distinct from semi-natural forests. Neither functional trait richness nor functional gene relative abundances responded clearly to urbanization or vegetation type. Despite functional redundancy, vegetation type did affect soil communities compositionally. Soils under trees producing recalcitrant litter had a higher richness of fungal species than the labile ones, whereas lawns, despite of their structural simplicity, had an unexpectedly high diversity of bacteria and fungi. In summary, despite distinct differences in the soil microbiota across biomes, urbanisation and vegetation type have similar effects on structuring microbial communities within biomes. However, the urban soil microbiota, irrespective of the plant functional type they associate with, are functionally comparable to those in semi-natural forests, suggesting functional redundancy within this unique microbiota.