The assessment and monitoring of biodiversity in urban areas has been shown to have enormous potential to inform integrative urban planning in cities. In this context, digital biodiversity repositories such as the Global Biodiversity Information Facility (GBIF) has been promoted for its central role in gathering and harmonizing biodiversity data worldwide, thereby facilitating these assessments and monitoring efforts. While GBIF data has been investigated for its potential at a large scale and in natural ecosystems, the question remains as to what extent, and in which context, is GBIF data applicable to urban biodiversity assessment and monitoring? In this study, we assessed the spatial patterns of biodiversity, by exploring species richness patterns in relation to land use types for three taxonomic groups (birds, mammals and arthropods) in three cities in The Netherlands (Rotterdam, Amsterdam and Groningen) at multiple spatial scales. We found significant variation in the effect of land uses on the species richness patterns, in terms of taxonomic group, spatial configuration and land cover type, and across spatial scales. Our study demonstrates the potential of GBIF data while highlighting the importance of the careful selection of one or multiple spatial scales, especially in relation to the taxonomic group characteristics and ecology and the spatial configuration of the cities studied.