Biodiversity change has elicited widespread concern over the consequences for functions and services provided by ecosystems1–3. Despite extensive evidence for a positive effect of biodiversity on ecosystem functioning within a single trophic level4,5, how this biodiversity effect varies with multi-trophic food web structure remains unresolved6 even though most ecosystems contain two to six trophic levels7. We investigate how food web complexity modulates biodiversity–ecosystem functioning relationships in nature by quantifying energy fluxes as proxies for two principal ecosystem functions8—primary consumption and predation—in 318 highly resolved, complex food webs from marine, lake, stream and soil ecosystems. Ecosystem functioning increased consistently with taxon richness across all trophic levels and ecosystems, which arose from greater vertical diversity (that is, maximum trophic level9) and trophic complementarity of predators in more taxonomically diverse food webs. Furthermore, predator trophic complementarity10,11 increased predation fluxes in all freshwater ecosystem types. These findings highlight the threat of trophic downgrading to critical ecosystem functions (for example, biological control and maintenance of biodiversity and ecosystem stability) provided by predators12,13, which are typically most vulnerable to anthropogenic disturbances14,15. Our study demonstrates that the consequences of biodiversity change are deeply entangled within the web of life, emphasizing the need to conserve the trophic complexity underlying biodiversity–ecosystem function relationships.
