Invertebrates have a central role in food webs and ecosystem functioning. By boosting productivity, allochthonous nutrient inputs influence the food webs of recipient communities. Understanding how allochthonous nutrient subsidies affect invertebrates is crucial, particularly in highly productive coastal areas. Here, we examine how mangrove macroinvertebrates are impacted by nutrient‐rich guano delivered by nesting seabird populations at Aldabra Atoll in the Indian Ocean. We compare nitrogen and carbon stable isotope ratios and nitrogen composition of basal resources and macroinvertebrate consumers in mangroves with and without nesting seabirds. Seabird‐derived nutrient enrichment increased the nitrogen content of basal food sources and herbivorous littorinid gastropods and sesarmid crabs. In mangroves with breeding seabirds, mean carapace widths of sesarmid and omnivorous portunid crabs were 6% and 11% larger, respectively. Isotopic niches of littorinid gastropods and sesarmid crabs were larger and had higher overlap at seabird compared to non‐seabird sites. Epiphytic macroalgae and guano comprised >50% of resource contributions to littorinid gastropods and sesarmid crabs at seabird sites. This differed markedly from non‐seabird sites where the main resource contributions were 77% mangrove leaves for littorinid gastropods, 36% sediment organic matter, and 41% mangrove leaves for sesarmid crabs. The increased sizes of mangrove crabs suggest that seabird nutrient enrichment can promote mangrove crab fisheries productivity and benefit the provisioning of mangrove ecosystem services. By shifting resource use of functionally important macroinvertebrates, we discuss how seabirds modify trophic interactions, with potential consequences for mangrove ecosystem processes and resilience.