Marine nutrients underpin productivity and functioning of oceanic island ecosystems. On islands where they nest, seabirds represent a primary source of marine nutrients. In tropical regions, some of the largest seabird populations nest on atolls, yet there is limited information available on seabird contributions to atoll ecosystem nutrient dynamics. To investigate the spatial and seasonal dynamics of seabird contributions, we assessed seabird colonies of different taxa, including red‐footed boobies and terns, nesting on separate islands of Farquhar Atoll, Seychelles. We assessed nutrient concentrations of guano, soil, coastal plants, and nearby seagrass in seabird colonies and at a control island with no seabirds, during the wet and dry seasons. Sooty terns contributed the highest quantities of nutrients, estimated at 71.2 N tonne/year and 52.2 P tonne/year. Seabird‐derived nutrient transfer occurred year‐round from seabird colonies to soil, coastal plants and seagrass. Soil macro‐ and inorganic nutrients were higher in the high‐density tern colony and during the dry season, coinciding with the breeding period of sooty terns. Both red‐footed booby and tern colonies maintained high nitrogen levels in coastal plants year‐round, while phosphorus levels did not differ between islands or seasons. Seabird‐derived nitrogen reversed nitrogen limitation of seagrass during the dry season. We provide the first insights into seabird nutrient contributions to atoll ecosystems in Seychelles, with recommendations for seabird conservation to boost and support atoll and island ecosystem resilience. Our results from a relatively undisturbed atoll serve as a baseline with which more impacted atolls and future changes can be assessed.