Urban biotic homogenization is one of the foremost challenges for conservation of biodiversity in urban green areas. Urban gardening is a common practice in many industrialised and developing countries. The ability of urban vegetable gardens to support biodiversity, however, has yet to be studied in depth. To investigate the responses of flora and soil fauna to urbanization, we surveyed the taxonomic and functional composition of plant and collembolan communities, in addition to soil parameters, in 15 urban vegetable gardens across three large French cities. The vegetation was identified in six plots of 1 × 1 m in each urban vegetable garden and collembolan were extracted from one intact soil core sampled in the center of each plot (5 cm depth, 6 cm diameter). We found contrasting effects of urbanization on plants and Collembola biodiversity. The taxonomic and functional composition of the soil fauna was more similar within cities than among cities, which was driven by similarities in soil parameters. In contrast, plant communities were functionally similar among cities. Understanding the effects of urbanization on soil biodiversity could have implications for the management of urban ecosystems, in particular that of urban soils.