This study describes the soil microbiome in relation to the aboveground plant diversity of three types of urban green spaces: built green spaces with sown lawns, planted trees and ornamental flowerbeds, open green spaces such as meadows and pastures, and urban forests. Data includes information on study sites, soil physio-chemical properties, vegetation, and soil microbiome: Plot information, Soil properties, Vegetation, Meta includes column information in sheets plot and soil. In vegetation sheet column names are species. Explanations for species name abbreviations can be found in sheet meta2. Micoboal commnity composition and taxonomy in Bacteria_nmds and Fungi_nmds.