Over 6-million pairs of sooty terns Sterna fuscata breed once a year in the southwest Indian Ocean, mostly on three islands of the Mozambique Channel (Europa, Juan de Nova and Glorieuses) and in the Seychelles region. Seasonal reproduction in either winter or summer is the dominant strategy in the area, but non-seasonal reproduction also occurred in some places like at Glorieuses Archipelago. The feeding ecology of the sooty tern was investigated during the breeding seasons to determine whether terns showed significant differences in their trophic ecology between locations. Regurgitations were analyzed to describe the diet of individuals when breeding, and stable isotopes and mercury concentrations were used to temporally integrate over the medium-term of the trophic ecology of both adults and chicks. Overall, the diet was composed of fish, flying squid and fish larvae in different proportions. At Europa and Aride in the Seychelles, where winter reproduction occurs, large epipelagic prey like flying fish or squid dominated the diet. At Juan de Nova, sooty terns reproduce in summer and rely mostly on fish larvae. At Glorieuses (non-seasonal breeding), the diet was intermediate with fish larvae and flying squid being important prey items. The stable-carbon and nitrogen isotope values in blood confirm the differences observed in dietary analysis, and demonstrate different feeding strategies between colonies. δ¹³C values of feathers showed spatial segregation between birds from the Mozambique Channel and the Seychelles region. Terns from the Seychelles had also higher δ¹⁵N values. Feather δ¹³C values also suggest a significant shift from summer to wintering habitat for birds from Juan de Nova. This study emphasizes the high phenotypic plasticity of the species, which may explain its numerical dominance in all tropical waters of the World’s Ocean.