Trophic cascades in which predatory organisms regulate organisms at lower trophic levels are important drivers of species dynamics, but effects of trophic cascades on ecosystem fluxes and processes, and the conditions under which top-down control is important, remain unresolved. We manipulated the structure of food webs in boreal mosses to show that moss-inhabiting microfauna exerted top-down control of N2-fixation by moss-associated cyanobacteria. However, organisms of higher trophic levels alleviated this top-down control, likely through feeding on bacterivorous microfauna. These effects of food web structure on cyanobacterial N2 fixation were dependent on global change factors and strongly suppressed under N fertilization. Our findings illustrate how food web interactions and trophic cascades can regulate boreal ecosystem N cycling. In boreal ecosystems, carbon uptake is generally strongly N-limited, and shifting trophic control of N cycling under global change is therefore likely to impact significantly on ecosystem functioning.