Green roofs, especially productive ones (e.g. of edible biomass), are urban ecosystems developed in response to the scarcity of arable areas in urban environments. Their installation is also perceived as a possible way to preserve biodiversity in cities. However, the effectiveness of green roofs in supporting biodiversity, especially soil biodiversity, has rarely been studied. In order to orient the ecological engineering of green roofs, it is crucial to understand the resulting biodiversity patterns. We hypothesised that a functional trait-based approach could be used to investigate different ways of colonisation. We investigated collembolan communities in both extensive and productive green roofs. Surprisingly, no difference was observed in either taxonomic or functional structures of collembolan diversity between extensive and productive green roofs. Conversely, according to the functional composition, two ways of colonisation are suggested: a passive wind dispersal − the “flying” collembolans − and a settlement through compost inputs. We conclude that stakeholders should take into account the spatial connections of green roofs with other green spaces in order to support soil biodiversity. Further studies are needed to more accurately elucidate the importance of green roof types for collembolan communities and associated ecological networks.