The benthic communities of soft-sediment intertidal ecosystems trophically underpin the migration of birds and fish. Within the East Atlantic Flyway, along the coast of West-Africa, the intertidal mudflats of Banc d’Arguin, Mauritania, host over 2 million migratory waterbirds. Despite the protected status of the Banc d’Arguin, geographical remoteness and seemingly benign human exploitation, we show that large changes have taken place in the intertidal benthic macrofauna across an interval of 28 years. We compared the results of two comparable and spatially comprehensive large-scale benthic surveys in 1986 and 2014. Over this time, the benthos changed from a diverse community to one dominated by a few species of bivalve, with a loss of polychaete worms. The change was associated with a twofold increase in the seagrass cover. Our results suggest that the intertidal habitats of Banc d’Arguin have altered markedly over the last three decades and the estimated benthic secondary production has decreased by a factor of four. These shifts in community structure and production may have contributed to declines in some benthivorous migratory shorebirds.