ABSTRACT Understanding the impact of ecological factors on biodiversity is central in the context of accelerating climate change and biodiversity loss. Urban areas, as landscapes under particularly strong anthropogenic influence, are undergoing rapid ecological change, yet the consequences for urban biodiversity and ecosystem functioning remain poorly understood. In this study, we focused on fruit flies of the genus Drosophila —a diverse group of dipterans with variable ecological niches and degrees of synanthropy, i.e., the adaptation to human‐modified habitats. We investigated species composition and community ecology in the metropolitan area of Vienna, Austria. With the help of numerous citizen scientists, we have collected approximately 18,000 specimens through dense spatio‐temporal sampling both indoors and outdoors of human dwellings. A total of 13 Drosophila species were identified, with communities dominated by widespread cosmopolitan synanthropic species. Among these, D. mercatorum and D. virilis represent novel records for Austria. Comparisons to a previous study from more than 30 years ago revealed that the species richness in Vienna was more than 50% lower than before and showed that formerly common species were potentially replaced by non‐indigenous drosophilids (neobiota). We further assessed ecological niches by intersecting species abundance data with high‐dimensional, high‐resolution earth observation datasets, which revealed distinct ecological preferences among species. In particular, the neozoan D. mercatorum emerged as a highly synanthropic species, tightly confined to urban areas with high levels of imperviousness. In summary, our study underpins the versatility of the Drosophila system as an indicator of biodiversity loss in a rapidly changing world.