Shorebirds and seabirds are abundant predators in coastal habitats worldwide, relying upon a high diversity of benthic invertebrates and fish, respectively. While occupying different trophic guilds, they are differently exposed to element contamination entering the coastal food web. Therefore, these birds have been used as bioindicators of environmental contamination in marine ecosystems. We analysed the concentration of trace elements in blood samples of 16 shorebird and seabird migratory species in a major non-breeding site, the Bijagós Archipelago, in regard to their trophic ecology. Overall, our study shows low exposure of this bird community to toxic elements, except for Hg. Most species presented Hg burdens within the moderate toxicity threshold, but one species (Dunlin) presented values at a potential high Hg toxicity risk. We found a positive relationship between Se and Ni concentrations and δ15N values (a proxy for trophic level). In addition, a positive relationship was found between δ13C (a proxy for habitat characteristics) and Hg, Fe, Cu and Mn, while the opposite pattern was recorded for As. Differences were also shown for several trace elements between the two studied trophic guilds: concentrations of As, Pb and Se were higher in pelagic fish consumers (seabirds), whereas Cr, Fe and Sr burdens were higher in benthic invertebrate consumers (shorebirds). Although previous studies in the same site revealed very high concentrations of Cd and Pb in some of the prey species of shorebirds and seabirds (bivalves and fishes), values found in birds for these two elements suggest no toxicological risk. Thus, exposure to toxic elements is not currently a threat to coastal bird populations, namely those facing apparent local declines in Guinea-Bissau, one of the most important non-breeding quarters for of West Africa. Still, Hg burdens were high in some species, deserving further monitoring. Display omitted •We present the first trace elements assessment on migratory birds in West Africa.•Most bird species were little exposed to toxic elements in the Bijagós Archipelago.•Dunlins are at a potential high Hg toxicity risk.•Se and Ni significantly increased with δ15N.•As, Pb and Se were higher in seabirds; Cr, Fe and Sr were higher in shorebirds.