Significance Ecosystem services derive from ecosystem functions and rely on complex interactions among a diversity of organisms. By understanding the relationships between biodiversity, ecosystem functions, and the services humans receive from nature, we can anticipate how changes in land use will affect ecosystems and human wellbeing. We show that increasing land-use intensity homogenizes the synergies between three organizational levels of the ecosystem, namely, biodiversity, ecosystem functions, and services. Increasing land-use intensity changes keystone components, which are important for the functioning of the ecosystem, and alters the synergies and trade-offs between biodiversity, ecosystem functions, and services. Our approach provides a comprehensive view of ecosystem functioning and can identify the key ecosystem attributes to monitor in order to prevent critical shifts in ecosystems.