Evidence of large‐scale biodiversity degradation in marine ecosystems has been reported worldwide, yet most research has focused on few species of interest or on limited spatiotemporal scales. Here we assessed the spatial and temporal changes in the taxonomic and functional composition of fish communities in European seas over the last 25 years (1994–2019). We then explored how these community changes were linked to environmental gradients and fishing pressure. We show that the spatial variation in fish species composition is more than two times higher than the temporal variation, with a marked spatial continuum in taxonomic composition and a more homogenous pattern in functional composition. The regions warming the fastest are experiencing an increasing dominance and total abundance of r‐strategy fish species (lower age of maturity). Conversely, regions warming more slowly show an increasing dominance and total abundance of K‐strategy species (high trophic level and late reproduction). Among the considered environmental variables, sea surface temperature, surface salinity and chlorophyll‐a most consistently influenced communities' spatial patterns, while bottom temperature and oxygen had the most consistent influence on temporal patterns. Changes in communities' functional composition were more closely related to environmental conditions than taxonomic changes. Our study demonstrates the importance of integrating community‐level species traits across multi‐decadal scales and across a large region to better capture and understand ecosystem‐wide responses and provides a different lens on community dynamics that could be used to support sustainable fisheries management.