Large‐scale alterations in marine ecosystems as a response to environmental and anthropogenic pressures have been documented worldwide. Yet, these are primarily investigated by assessing abundance fluctuations of a few dominant species, which inadequately reflect ecosystem‐wide changes. In addition, it is increasingly recognized that it is not species identity per se, but their traits that determine environmental responses, biological interactions and ecosystem functioning. In this study, we investigated long‐term, spatio‐temporal variability in trait composition across multiple organism groups to assess whether functional changes occur in a similar way across trophic levels and whether shifts in trait composition link to environmental change. We combined extensive trait datasets with long‐term surveys (30–40 yr) of four organism groups (phytoplankton, zooplankton, benthic invertebrates and fish) in three environmentally distinct areas of a large marine ecosystem. We found similar temporal trajectories in the community weighted mean trait time‐series of the different trophic groups, revealing ecosystem‐wide functional changes. The traits involved and their dynamics differed between areas, concurrent with climate‐driven changes in temperature and salinity, as well as more local dynamics in nutrients and oxygen. This finding highlights the importance of considering both global climate, as well as local external drivers when studying ecosystem changes. Using a multi‐trophic trait‐based approach, our study demonstrates the importance of integrating community functional dynamics across multiple trophic levels to capture ecosystem‐wide responses which could, ultimately, help moving towards a holistic understanding, assessment and management of marine ecosystems.